Shifts in microbial communities driven by the succession of seagrasses to benthic macroalgae may exacerbate heatwave effects in eutrophicated-coastal lagoons: Statistical analysis

This document contains all statistical analyses conducted for the manuscript.
All data to reproduce analysis can be found here: https://github.com/biocom-uib/CAUvsCYM. This document uses precomputed data for heavy calculations. See README for details.

1 Setup

rm(list = ls())
knitr::opts_chunk$set(
   fig.width=10, 
  out.width="50%",
  fig.asp = 1,
  fig.align="center",
  echo = TRUE,
  message = FALSE, 
  warning = FALSE,
  hiline = TRUE,
  cache=TRUE
)
options(knitr.kable.NA = '')
knitr::opts_knit$set(global.par=TRUE)
par(cex.main=0.9,cex.axis=0.8,cex.lab=0.8)
options(scipen = 999)

We load the necessary packages:

library(readxl)
library(readr)
library(dplyr)
library(tidyr)
library(knitr)
library(ggplot2)
library(grid)
library(tidyverse)
library(splines)
library(zCompositions)
library(compositions)
library(robCompositions)
library(easyCODA)
library(ALDEx2)
library(viridis)
library(plotly)
library(ComplexHeatmap)
library(stats)
library(dendextend)
library(RColorBrewer)
library(kableExtra)
library(vegan)
library(ecolTest)
library(factoextra)
library(coda4microbiome)
library(broom)
source("funcionsCODAMETACIRCLE.R")


opar=par()

library(flextable)
set_flextable_defaults(
  font.family = "Arial", font.size = 10, 
  border.color = "gray", big.mark = "")

2 Statistical analysis of biochemical and cellular parameters

2.1 Sulfur concentrations

#Data and factors 
datos <- read_table("Sulfur_data_28ago25.txt")
datos$Species<-as.factor(datos$Species)
datos$Treatment<-as.factor(datos$Treatment)
datos$Time<-factor(datos$Time, levels = c("T0", "T2"))

#Group summary for plotting 
df_summary <- datos %>%
  group_by(Time, Species, Treatment) %>%
  summarise(
    mean_sulfur = mean(Sulfur, na.rm = TRUE),
    sd_sulfur   = sd(Sulfur, na.rm = TRUE),
    n           = n(),
    se_sulfur   = sd_sulfur / sqrt(n)
  ) %>%
  ungroup()

# --- Figure (as in the paper: means ± SE) ---
p_a<- ggplot() +
  geom_jitter(data = datos,
              aes(x = Time, y = Sulfur, color = Species, 
                  shape = Treatment),
              width = 0.1,  
              alpha = 0.4,
              size = 1.2) +
  geom_line(data = df_summary,
            aes(x = Time, 
                y = mean_sulfur, 
                color = Species, 
                group = interaction(Species, Treatment),
                linetype = Treatment),
            size = 1) +
  geom_point(data = df_summary,
             aes(x = Time, 
                 y = mean_sulfur, 
                 color = Species, 
                 shape = Treatment),
             size = 3) +
  geom_errorbar(data = df_summary,
                aes(x = Time, 
                    ymin = mean_sulfur - se_sulfur,
                    ymax = mean_sulfur + se_sulfur,
                    color = Species),
                width = 0.1,
                size = 1.2) +
  scale_color_manual(values = c("CAU" = "#008ae6", "CYM" = "#ff751a")) +
  labs(
    x = "Time",
    y = expression(paste("Sulfur (", mu, "M)")),
    color = "Species",
    shape = "Treatment",
    linetype = "Treatment"
  ) +
  theme_minimal() +
  theme(axis.title.x = element_text(face = "bold"),
        axis.title.y = element_text(face = "bold"),
        axis.text.x  = element_text(face = "bold"),
        legend.title = element_text(face = "bold")
        ) +
  coord_cartesian(ylim = c(400, 1400)) +  
  scale_y_continuous(
    breaks = seq(400, 1400, by = 100)      
  ) 

p_a

The figure shows sulfur concentrations (mean ± SE) at baseline (T0) and after exposure (T2) for sediments colonized by Caulerpa (blue) and Cymodocea (orange) under control (solid lines) and heatwave (dashed lines) conditions. In both species, sulfur levels increased from T0 to T2. The increase was evident under both control and heatwave treatments in Caulerpa, whereas in Cymodocea the rise was more pronounced under heatwave conditions. Individual data points (faded symbols) illustrate the variability within groups.

To evaluate changes in sediment sulfur concentration, we applied a nonparametric testing framework. First, we examined within-group temporal changes (T0 vs T2) separately for each Species × Treatment using Wilcoxon tests, with p-values adjusted by the Benjamini–Hochberg procedure. We then compared treatments at T2 (Control vs Heatwave) within each species to assess whether heatwave exposure altered sulfur at the final time point. This two-step approach provides both temporal (within-group) and treatment-level (between-group) perspectives on sulfur dynamics.

We first report group medians at T0 and T2 and their difference (Δ = T2 − T0) for each Species × Treatment. These summaries are descriptive and motivate the subsequent nonparametric tests.

medians <- datos %>%
  group_by(Species, Treatment, Time) %>%
  summarise(median_sulfur = median(Sulfur, na.rm = TRUE), n = dplyr::n(), .groups = "drop") %>%
  tidyr::pivot_wider(names_from = Time, values_from = median_sulfur) %>%
  # Opción A: con comillas invertidas (recomendado)
  mutate(delta_median = `T2` - `T0`)
  # Opción B (alternativa robusta):
  # mutate(delta_median = get("T2") - get("T0"))

knitr::kable(medians, digits = 2, caption = "Medians by group and change (T2 - T0)")

Table 1: Medians by group and change (T2 - T0)

Species	Treatment	n	T0	T2	delta_median
CAU	Control	9	945.91	1151.37	205.46
CAU	HW	9	939.62	1284.93	345.31
CYM	Control	9	785.53	894.56	109.03
CYM	HW	9	835.85	1109.06	273.21

We then formally tested T0 vs T2 within each Species × Treatment using Wilcoxon rank–sum tests, controlling the false discovery rate with Benjamini–Hochberg adjustment.

time_tests <- datos %>%
  dplyr::group_by(Species, Treatment) %>%
  dplyr::summarise(
    p = {
      d <- dplyr::cur_data()
      x <- d$Sulfur[d$Time == "T0"]
      y <- d$Sulfur[d$Time == "T2"]
      if (length(x) > 0 && length(y) > 0) {
        suppressWarnings(stats::wilcox.test(x, y, exact = FALSE)$p.value)
      } else {
        NA_real_
      }
    },
    .groups = "drop"
  ) %>%
  dplyr::mutate(p_adj = p.adjust(p, method = "BH"))

knitr::kable(time_tests, digits = 3,
             caption = "Wilcoxon (T0 vs T2) per Species × Treatment (BH-adjusted p)")

Table 2: Wilcoxon (T0 vs T2) per Species × Treatment (BH-adjusted p)

Species	Treatment	p	p_adj
CAU	Control	0.008	0.011
CAU	HW	0.001	0.002
CYM	Control	0.158	0.158
CYM	HW	0.004	0.007

These outputs provide a basis for the statement that sulfur increased in both species and that the rise was more pronounced under heatwave conditions—particularly for Cymodocea at T2.

2.1.1 Difference-in-Differences (DiD) models

To complement the nonparametric analyses and jointly assess the effects of time and treatment, a difference-in-differences (DiD) model was applied separately for each species. This approach makes it possible to test whether the temporal change in sulfur differs significantly between control and heatwave conditions, while accounting for the main effects of treatment and time. In particular, the interaction term (Treatment × Time) captures the differential effect attributable to the heatwave at the final time point (TF), thus providing a direct measure of the magnitude of the treatment impact in each species.

Cymodocea — sulfur analysis

cy <- datos %>%
  dplyr::filter(Species == "CYM")

cy$Treatment <- factor(cy$Treatment, levels = c("Control", "HW"))
cy$Time      <- factor(cy$Time,      levels = c("T0", "T2"))

fit_cy <- lm(Sulfur ~ Treatment + Time + Treatment:Time, data = cy)
summary(fit_cy)

## 
## Call:
## lm(formula = Sulfur ~ Treatment + Time + Treatment:Time, data = cy)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -318.31 -118.50   32.97   95.49  266.60 
## 
## Coefficients:
##                    Estimate Std. Error t value           Pr(>|t|)    
## (Intercept)          720.20      56.15  12.826 0.0000000000000372 ***
## TreatmentHW           21.73      79.41   0.274             0.7861    
## TimeT2               163.62      79.41   2.061             0.0476 *  
## TreatmentHW:TimeT2   129.66     112.30   1.155             0.2568    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 168.5 on 32 degrees of freedom
## Multiple R-squared:  0.3877, Adjusted R-squared:  0.3303 
## F-statistic: 6.754 on 3 and 32 DF,  p-value: 0.001172

In Cymodocea, sulfur concentrations increased significantly from T0 to T2 under control conditions (Time effect: p = 0.048). The DiD model further estimated an additional increase under heatwave exposure at T2 (interaction coefficient = 129.7), consistent with the descriptive pattern of a more pronounced rise under heatwave conditions. However, this differential effect was not statistically significant (p = 0.26), indicating that while the data suggest a stronger increase in Cymodocea under heatwave exposure, statistical support for this effect remains moderate.

Caulerpa — sulfur analysis

ca <- datos %>%
  dplyr::filter(Species == "CAU")

ca$Treatment <- factor(cy$Treatment, levels = c("Control", "HW"))
ca$Time      <- factor(cy$Time,      levels = c("T0", "T2"))

fit_ca <- lm(Sulfur ~ Treatment + Time + Treatment:Time, data = ca)
summary(fit_ca)

## 
## Call:
## lm(formula = Sulfur ~ Treatment + Time + Treatment:Time, data = ca)
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -242.770  -71.945   -7.951   83.563  226.415 
## 
## Coefficients:
##                    Estimate Std. Error t value             Pr(>|t|)    
## (Intercept)         955.346     40.921  23.346 < 0.0000000000000002 ***
## TreatmentHW          -1.572     57.872  -0.027             0.978493    
## TimeT2              222.755     57.872   3.849             0.000534 ***
## TreatmentHW:TimeT2  114.871     81.843   1.404             0.170080    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 122.8 on 32 degrees of freedom
## Multiple R-squared:  0.6131, Adjusted R-squared:  0.5769 
## F-statistic: 16.91 on 3 and 32 DF,  p-value: 0.0000009271

In Caulerpa, sulfur concentrations increased significantly from T0 to T2 under control conditions (Time effect: p < 0.001). The DiD model further estimated an additional increase under heatwave exposure at T2 (interaction coefficient = 114.9), consistent with the descriptive pattern of greater accumulation under heatwave conditions. However, this differential effect was not statistically significant (p = 0.17), indicating that while sulfur accumulation clearly occurred over time, the evidence for an extra increase driven by heatwave exposure remains moderate.

2.2 Redox potential

#Data
datos <- read_table("redox_data_12feb25.txt")
datos$Species<-as.factor(datos$Species)
datos$Treatment<-as.factor(datos$Treatment)
datos$Time<-factor(datos$Time, levels = c("T0", "T2"))

#Group summary for plotting
df_summary <- datos %>%
  group_by(Time, Species, Treatment) %>%
  summarise(
    mean_redox = mean(redox, na.rm = TRUE),
    sd_redox   = sd(redox, na.rm = TRUE),
    n           = n(),
    se_redox   = sd_redox / sqrt(n)
  ) %>%
  ungroup()


p_b <- ggplot() +
  geom_jitter(data = datos,
              aes(x = Time, y = redox, color = Species, shape = Treatment),
              width = 0.1,  
              alpha = 0.4,
              size = 1.2) +
  
  geom_line(data = df_summary,
            aes(x = Time, 
                y = mean_redox, 
                color = Species, 
                group = interaction(Species, Treatment),
                linetype = Treatment),
            size = 1) +
  geom_point(data = df_summary,
             aes(x = Time, 
                 y = mean_redox, 
                 color = Species, 
                 shape = Treatment),
             size = 3) +
  geom_errorbar(data = df_summary,
                aes(x = Time, 
                    ymin = mean_redox - se_redox,
                    ymax = mean_redox + se_redox,
                    color = Species),
                width = 0.1,
                size = 1.2) +
  scale_color_manual(values = c("CAU" = "#008ae6", "CYM" = "#ff751a")) +
  labs(
    x = "Time",
    y = expression(paste("redox (",m, "M)")) ,
    color = "Species",
    shape = "Treatment",
    linetype = "Treatment"
  ) +
  theme_minimal() + 
  theme(axis.title.x = element_text(face = "bold"),
         axis.title.y = element_text(face = "bold"),
        axis.text.x  = element_text(face = "bold"),
        legend.title = element_text(face = "bold")
        ) +
   coord_cartesian(ylim = c(-430, -330)) +  
   scale_y_continuous(
     breaks = seq(-430, -330, by = 10)      
   )
p_b

The figure shows sediment redox potential (mean ± SE) at baseline (T0) and after exposure (T2) for sediments colonized by Caulerpa (blue) and Cymodocea (orange) under control (solid lines) and heatwave (dashed lines) conditions. In Caulerpa, redox potential declined significantly from T0 to T2 under control conditions but remained stable under heatwave conditions. In Cymodocea, redox potential also decreased over time, with a stronger decline under heatwave treatment.

To evaluate changes in sediment redox potential, we applied a nonparametric testing framework. First, we examined within-group temporal changes (T0 vs T2) separately for each Species × Treatment using Wilcoxon tests, with p-values adjusted by the Benjamini–Hochberg procedure. We then compared treatments at T2 (Control vs Heatwave) within each species to assess whether heatwave exposure altered redox potential at the final time point. This two-step approach provides both temporal (within-group) and treatment-level (between-group) perspectives on redox dynamics.

We present a nonparametric analysis of sediment redox potential. First, we assess within-group change from T0 to T2 for each Species × Treatment using Wilcoxon tests and compare treatments at T2 within each species. P-values are adjusted for multiple testing with the Benjamini–Hochberg procedure

eh_within <- datos %>%
  dplyr::group_by(Species, Treatment) %>%
  dplyr::summarise(
    p = {
      d <- dplyr::cur_data()
      x <- d$redox[d$Time == "T0"]
      y <- d$redox[d$Time == "T2"]
      if (length(x) > 0 && length(y) > 0) {
        suppressWarnings(stats::wilcox.test(x, y, exact = FALSE)$p.value)
      } else NA_real_
    },
    .groups = "drop"
  ) %>%
  dplyr::mutate(p_adj = p.adjust(p, method = "BH"))

knitr::kable(eh_within, digits = 3,
             caption = "Wilcoxon (T0 vs T2) by Species × Treatment (BH-adjusted p)")

Table 3: Wilcoxon (T0 vs T2) by Species × Treatment (BH-adjusted p)

Species	Treatment	p	p_adj
CAU	Control	0.005	0.020
CAU	HW	0.575	0.575
CYM	Control	0.298	0.397
CYM	HW	0.045	0.091

These summaries show that redox potential generally decreased over time, with the largest declines occurring in Caulerpa under control conditions and in Cymodocea under heatwave conditions. These descriptive patterns motivated the subsequent nonparametric tests.

eh_t2_bt <- datos %>%
  dplyr::filter(Time == "T2") %>%
  dplyr::group_by(Species) %>%
  dplyr::summarise(
    p = {
      d <- dplyr::cur_data()
      if (dplyr::n_distinct(d$Treatment) >= 2) {
        suppressWarnings(stats::wilcox.test(redox ~ Treatment, data = d, exact = FALSE)$p.value)
      } else NA_real_
    },
    .groups = "drop"
  ) %>%
  dplyr::mutate(p_adj = p.adjust(p, method = "BH"))

knitr::kable(eh_t2_bt, digits = 3,
             caption = "Wilcoxon (Treatment) at T2 by Species (BH-adjusted p)")

Table 4: Wilcoxon (Treatment) at T2 by Species (BH-adjusted p)

Species	p	p_adj
CAU	0.298	0.298
CYM	0.045	0.091

Overall, redox potential tended to decrease from T0 to T2, but the magnitude and significance of these shifts varied across species and treatments. In Caulerpa, a significant decline was detected under control conditions (BH-adjusted p = 0.020), whereas no change was observed under heatwave conditions. In Cymodocea, redox potential also decreased over time, with a trend towards stronger reductions under heatwave exposure (raw p = 0.045), though this did not remain significant after correction (BH-adjusted p = 0.091). Comparisons between treatments at T2 revealed no differences for Caulerpa and only a marginal effect for Cymodocea (BH-adjusted p = 0.091).

2.2.1 Difference-in-Differences (DiD) models

We fitted difference-in-differences (DiD) models for each species. This framework evaluates whether changes in redox potential from T0 to T2 differed between control and heatwave conditions, while simultaneously accounting for the main effects of treatment and temporal progression. The key parameter of interest is the interaction term (Treatment × Time), which quantifies the additional effect attributable to heatwave exposure at the final sampling point (T2), thereby offering a direct estimate of the treatment-specific impact.

Cymodocea — redox analysis

fit_cy <- lm(Redox ~ Treatment + Time + Treatment:Time, data = cy)
summary(fit_cy)

## 
## Call:
## lm(formula = Redox ~ Treatment + Time + Treatment:Time, data = cy)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -42.133 -13.897  -2.578  10.992  58.667 
## 
## Coefficients:
##                    Estimate Std. Error t value            Pr(>|t|)    
## (Intercept)        -367.567      6.886 -53.382 <0.0000000000000002 ***
## TreatmentHW           3.100      9.738   0.318              0.7523    
## TimeT2              -20.711      9.738  -2.127              0.0412 *  
## TreatmentHW:TimeT2  -19.089     13.771  -1.386              0.1753    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 20.66 on 32 degrees of freedom
## Multiple R-squared:  0.4086, Adjusted R-squared:  0.3531 
## F-statistic: 7.368 on 3 and 32 DF,  p-value: 0.000689

In Cymodocea, redox potential declined significantly from T0 to T2 under control conditions (Time effect: –20.7, p = 0.041). The DiD model further estimated an additional reduction under heatwave exposure at T2 (interaction coefficient = –19.1), consistent with the descriptive observation of stronger declines under heatwave conditions. However, this interaction was not statistically significant (p = 0.18), indicating that while the data suggest a heatwave-driven intensification of the temporal decline in redox potential, the statistical support for this effect remains limited.

Caulerpa — redox analysis

fit_ca <- lm(Redox ~ Treatment + Time + Treatment:Time, data = ca)
summary(fit_ca)

## 
## Call:
## lm(formula = Redox ~ Treatment + Time + Treatment:Time, data = ca)
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -28.3444 -11.2625   0.1944   7.6500  30.1556 
## 
## Coefficients:
##                    Estimate Std. Error t value            Pr(>|t|)    
## (Intercept)        -392.850      4.974 -78.977 <0.0000000000000002 ***
## TreatmentHW         -13.794      7.035  -1.961              0.0586 .  
## TimeT2               -6.506      7.035  -0.925              0.3620    
## TreatmentHW:TimeT2    1.817      9.948   0.183              0.8563    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 14.92 on 32 degrees of freedom
## Multiple R-squared:  0.2002, Adjusted R-squared:  0.1252 
## F-statistic:  2.67 on 3 and 32 DF,  p-value: 0.06413

In Caulerpa, redox potential showed no significant temporal change from T0 to T2 under control conditions (Time effect: –6.5, p = 0.36). The model estimated a slightly lower baseline under heatwave compared to control at T0 (Treatment effect: –13.8, p = 0.059), suggesting a marginal initial difference between treatments. However, the interaction term (Treatment × Time) was small and not significant (p = 0.86), indicating that heatwave exposure did not alter the temporal trajectory of redox potential. Overall, these results suggest that, unlike Cymodocea, the decline in redox observed in Caulerpa sediments was not exacerbated by heatwave conditions.

2.3 Cellular parameters

We analyzed cell counts in sediments colonized by either Caulerpa or Cymodocea under control and heatwave conditions, assessing temporal changes (T0–T1–T2) within each Species × Treatment group as well as differences between species.

#Data
datos <- read_table("cell_shanon_data_12_05_25.txt") %>% 
  mutate(
    Species   = factor(Species),
    Time      = factor(Time, levels = c("T0","T1","T2")),
    Treatment = factor(Treatment),
    cells     = as.numeric(cells)
  )

#Group summary for plotting
summary_data <- datos %>%
  group_by(Species, Treatment, Time) %>%
  summarise(
    mean_cells = mean(cells, na.rm = TRUE),
    sd         = sd(cells,   na.rm = TRUE),
    n          = n(),
    se         = sd / sqrt(n),
    .groups    = "drop"
  )

t1_hw <- summary_data %>% 
  filter(Treatment == "HW", Time == "T1") %>%
  select(Species, y    = mean_cells)
t2_hw <- summary_data %>% 
  filter(Treatment == "HW", Time == "T2") %>%
  select(Species, yend = mean_cells)
segments_hw <- left_join(t1_hw, t2_hw, by = "Species")

t12     <- summary_data %>% filter(Time %in% c("T1","T2"))
rango12 <- range(t12$mean_cells - t12$se, t12$mean_cells + t12$se)
ymin12  <- rango12[1] - 0.025 * diff(rango12)
ymax12  <- rango12[2] + 0.025 * diff(rango12)


p_c<- ggplot() +
  geom_jitter(
    data  = datos,
    aes(x = Time, y = cells, color = Species, shape = Treatment),
    width = 0.1, alpha = 0.4, size = 1.2
  ) +
  geom_line(
    data = summary_data,
    aes(x = Time, y = mean_cells,
        color    = Species,
        linetype = Treatment,
        group    = interaction(Species, Treatment)),
    size = 1
  ) +
  geom_point(
    data  = summary_data,
    aes(x = Time, y = mean_cells, color = Species, shape = Treatment),
    size = 3
  ) +
  geom_errorbar(
    data = summary_data,
    aes(x = Time,
        ymin  = mean_cells - se,
        ymax  = mean_cells + se,
        color = Species),
    width = 0.2, size = 1.25
  ) +
  geom_segment(
    data      = summary_data,
    aes(y     = 53800000,
        yend  = 38700000,
        color = "CYM"),
    x      = 2,      
    xend   = 3,     
    linetype = "dashed",
    size      = 1.5
  ) +
  geom_segment(
    data      = summary_data,
    aes(y     = 173333333,
        yend  = 212000000,
        color = "CAU"),
    x      = 2,     
    xend   = 3,     
    linetype = "dashed",
    size      = 1.5
  ) +
  scale_color_manual(name   = "Species",
                     values = c("CAU" = "#008ae6", "CYM" = "#ff751a")) +
  scale_shape_manual(name   = "Treatment",
                     values = c("Control" = 16,  # circles filled
                                "HW"      = 17)) +# triangles filled
  scale_linetype_manual(name   = "Treatment",
                        values = c("Control" = "solid",
                                   "HW"      = "dashed")) +
  guides(
    shape    = guide_legend(override.aes = list(size = 3)),
    linetype = guide_legend(override.aes = list(size = 1.5))
  ) +
  labs(
    x        = "Time",
    y        = "Cells",
    color    = "Species",
    shape    = "Treatment",
    linetype = "Treatment"
  ) +
  theme_minimal(base_size = 12) +
  theme(
    axis.title.x = element_text(face = "bold"),
    axis.title.y = element_text(face = "bold"),
    axis.text.x  = element_text(face = "bold"),
    legend.title = element_text(face = "bold")
  ) +
  coord_cartesian(ylim = c(ymin12, ymax12)) +
  scale_y_continuous(
    breaks = pretty(c(ymin12, ymax12), n = 5),
    labels = expression(0,5%*%10^7,1%*%10^8,1.5%*%10^8,2%*%10^8,2.5%*%10^8),
    expand = expansion(mult = c(0,0))
  )

p_c

The figure shows cell counts in sediments colonized by Caulerpa (blue) and Cymodocea (orange) under control (solid lines) and heatwave (dashed lines) conditions across three time points (T0, T1, T2). In Caulerpa, cell numbers remained relatively stable from T0 to T1, followed by a marked increase under heatwave conditions at T2, while control samples decreased slightly. In contrast, Cymodocea exhibited consistently lower cell counts overall, with values remaining stable between T0 and T1 but declining toward T2 under both treatments, particularly under heatwave exposure.

We first quantified the overall range of cell counts observed in each species to provide context for the magnitude of the differences.

ranges <- datos %>%
  group_by(Species) %>%
  summarise(
    min_cells = min(cells, na.rm = TRUE),
    max_cells = max(cells, na.rm = TRUE),
    .groups = "drop"
  ) %>%
  mutate(min_x1e9 = round(min_cells / 1e9, 1),
         max_x1e9 = round(max_cells / 1e9, 1))

knitr::kable(ranges, digits = 2, caption = "Species-wise ranges (×10^9 cells/g)")

Table 5: Species-wise ranges (×10^9 cells/g)

Species	min_cells	max_cells	min_x1e9	max_x1e9
CAU	116000000	221000000	0.1	0.2
CYM	19800000	61900000	0.0	0.1

These ranges highlight the broader scale of variation in Caulerpa compared with Cymodocea, providing a baseline for interpreting subsequent tests.

To evaluate species-level differences, we first applied a Wilcoxon rank–sum test pooling across all time points and treatments.

# Overall (pooling all times/treatments)
bt_overall <- suppressWarnings(stats::wilcox.test(cells ~ Species, data = datos, exact = FALSE))

# By time (T0, T1, T2) — useful to show consistency
bt_by_time <- datos %>%
  group_by(Time) %>%
  summarise(
    p = {
      d <- cur_data()
      suppressWarnings(stats::wilcox.test(d$cells ~ d$Species, exact = FALSE)$p.value)
    },
    .groups = "drop"
  )

knitr::kable(bt_by_time, digits = 3, caption = "Between-species Wilcoxon by Time")

Table 6: Between-species Wilcoxon by Time

Time	p
T0	0.081
T1	0.081
T2	0.005

bt_overall$p.value

## [1] 0.00003658455

This overall comparison indicated that species differ in cell counts.

To assess whether cell counts changed over time within each Species × Treatment combination, we first applied a nonparametric global test across the three sampling points (T0, T1, T2).

# Kruskal–Wallis per group
kw_time <- datos %>%
  group_by(Species, Treatment) %>%
  summarise(
    kw_p = {
      d <- cur_data()
      if (n_distinct(d$Time) >= 2) {
        suppressWarnings(kruskal.test(cells ~ Time, data = d)$p.value)
      } else NA_real_
    },
    .groups = "drop"
  )

# Pairwise Wilcoxon per group (BH across the 3 pairwise contrasts within each group)
pw_time <- datos %>%
  group_by(Species, Treatment) %>%
  group_modify(~{
    d <- .x
    # Need at least 2 time levels
    if (n_distinct(d$Time) < 2) return(tibble())
    pw <- pairwise.wilcox.test(d$cells, d$Time, p.adjust.method = "BH", exact = FALSE)
    # Convert p-value matrix to long
    M <- as.data.frame(as.table(pw$p.value))
    names(M) <- c("Time1","Time2","p_adj")
    M <- M %>% filter(!is.na(p_adj))
    # Add direction using medians
    meds <- d %>% group_by(Time) %>% summarise(med = median(cells, na.rm = TRUE), .groups="drop")
    M <- M %>%
      left_join(meds, by = c("Time1" = "Time")) %>% rename(med1 = med) %>%
      left_join(meds, by = c("Time2" = "Time")) %>% rename(med2 = med) %>%
      mutate(direction = case_when(
        med2 > med1 ~ "increase",
        med2 < med1 ~ "decrease",
        TRUE ~ "no_change"
      ))
    M
  }) %>%
  ungroup()

knitr::kable(kw_time, digits = 3, caption = "Kruskal–Wallis across T0–T1–T2 by Species × Treatment")

Table 7: Kruskal–Wallis across T0–T1–T2 by Species × Treatment

Species	Treatment	kw_p
CAU	Control	0.491
CAU	HW
CYM	Control	0.193
CYM	HW

knitr::kable(pw_time, digits = 3, caption = "Pairwise Wilcoxon (BH-adjusted) and median directions")

Table 7: Pairwise Wilcoxon (BH-adjusted) and median directions

Species	Treatment	Time1	Time2	p_adj	med1	med2	direction
CAU	Control	T1	T0	0.663	168000000	159000000	decrease
CAU	Control	T2	T0	0.663	148000000	159000000	increase
CAU	Control	T2	T1	0.663	148000000	168000000	increase
CYM	Control	T1	T0	1.000	52400000	54000000	increase
CYM	Control	T2	T0	0.286	26500000	54000000	increase
CYM	Control	T2	T1	0.286	26500000	52400000	increase

Although the nonparametric tests did not detect statistically significant within-group changes, the descriptive patterns in the figures suggest some biologically meaningful trends. In particular, Cymodocea under control conditions showed a consistent rise in median cell counts from T0 to T2, and Caulerpa exhibited fluctuations that point to a potential increase by the final time point. The absence of statistical significance likely reflects the limited sample size and variability within groups, rather than a complete lack of temporal dynamics. Thus, while the formal tests provide little evidence for strong within-group effects, the graphical trends indicate subtle trajectories that may become clearer with larger sample sizes or longer experimental follow-up.

3 Biodiversity

Shannon diversity indices were computed with the diversity function in vegan and summarized by Species × Treatment × Time. We first visualized mean trajectories (±SE) together with individual observations to inspect temporal patterns and treatment contrasts.

library(readr)
library(dplyr)
library(ggplot2)
library(grid)    

datos <- read_table("cell_shanon_data_12_05_25.txt") %>% 
  mutate(
    Species   = factor(Species),
    Time      = factor(Time, levels = c("T0","T1","T2")),
    Treatment = factor(Treatment),
    shanon     = as.numeric(shanon)
  )

summary_data <- datos %>%
  group_by(Species, Treatment, Time) %>%
  summarise(
    mean_shanon = mean(shanon, na.rm = TRUE),
    sd         = sd(shanon,   na.rm = TRUE),
    n          = n(),
    se         = sd / sqrt(n),
    .groups    = "drop"
  )


t1_hw <- summary_data %>% 
  filter(Treatment == "HW", Time == "T1") %>%
  select(Species, y    = mean_shanon)
t2_hw <- summary_data %>% 
  filter(Treatment == "HW", Time == "T2") %>%
  select(Species, yend = mean_shanon)
segments_hw <- left_join(t1_hw, t2_hw, by = "Species")


t12     <- summary_data %>% filter(Time %in% c("T1","T2"))
rango12 <- range(t12$mean_shanon - t12$se, t12$mean_shanon + t12$se)
ymin12  <- rango12[1] - 0.55 * diff(rango12)
ymax12  <- rango12[2] + 0.25 * diff(rango12)


p_d<- ggplot() +
  geom_jitter(
    data  = datos,
    aes(x = Time, y = shanon, color = Species, shape = Treatment),
    width = 0.1, alpha = 0.4, size = 1.2
  ) +
  geom_line(
    data = summary_data,
    aes(x = Time, y = mean_shanon,
        color    = Species,
        linetype = Treatment,
        group    = interaction(Species, Treatment)),
    size = 1
  ) +
  geom_point(
    data  = summary_data,
    aes(x = Time, y = mean_shanon, color = Species, shape = Treatment),
    size = 3
  ) +
  geom_errorbar(
    data = summary_data,
    aes(x = Time,
        ymin  = mean_shanon - se,
        ymax  = mean_shanon + se,
        color = Species),
    width = 0.2, size = 1.25
  ) +
  geom_segment(
    data      = summary_data,
    aes(y     = 5.072667,
        yend  = 5.056000,
        color = "CYM"),
    x      = 2,     
    xend   = 3,      
    linetype = "dashed",
    size      = 1.5
  ) +
  geom_segment(
    data      = summary_data,
    aes(y     = 5.201667,
        yend  = 5.180333,
        color = "CAU"),
    x      = 2,     
    xend   = 3,      
    linetype = "dashed",
    size      = 1.5
  ) +
  scale_color_manual(name   = "Species",
                     values = c("CAU" = "#008ae6", "CYM" = "#ff751a")) +
  scale_shape_manual(name   = "Treatment",
                     values = c("Control" = 16,  # circles filled
                                "HW"      = 17)) +# triangles filled
  scale_linetype_manual(name   = "Treatment",
                        values = c("Control" = "solid",
                                   "HW"      = "dashed")) +
  guides(
    shape    = guide_legend(override.aes = list(size = 3)),
    linetype = guide_legend(override.aes = list(size = 1.5))
  ) +
  labs(
    x        = "Time",
    y        = "Shannon diversity index",
    color    = "Species",
    shape    = "Treatment",
    linetype = "Treatment"
  ) +
  theme_minimal(base_size = 12) +
  theme(
    axis.title.x = element_text(face = "bold"),
    axis.title.y = element_text(face = "bold"),
    axis.text.x  = element_text(face = "bold"),
    legend.title = element_text(face = "bold")
  ) +
  coord_cartesian(ylim = c(ymin12, ymax12)) +
  scale_y_continuous(
    breaks = pretty(c(ymin12, ymax12), n = 5),
    expand = expansion(mult = c(0,0))
  ) 
p_d

The plot shows that Caulerpa maintains relatively high and stable diversity across the experiment, with only slight changes between T1 and T2. Cymodocea exhibits a marked rise from T0 to T1, followed by a modest leveling or decline toward T2 under heatwave exposure, while control samples remain comparatively stable. These descriptive trends motivated formal between-species comparisons.

To test whether species differed in Shannon diversity, we applied Wilcoxon rank–sum tests overall (pooling time points) and separately at each sampling time.

## Overall (all times + treatments pooled)
bt_overall <- suppressWarnings(stats::wilcox.test(shanon ~ Species, data = datos, exact = FALSE))
bt_overall_p <- bt_overall$p.value

## By time (T0, T1, T2)
bt_by_time <- datos %>%
  group_by(Time) %>%
  summarise(
    med_CAU = median(shanon[Species == "CAU"], na.rm = TRUE),
    med_CYM = median(shanon[Species == "CYM"], na.rm = TRUE),
    p = {
      d <- cur_data()
      suppressWarnings(stats::wilcox.test(d$shanon ~ d$Species, exact = FALSE)$p.value)
    },
    .groups = "drop"
  )

kable(bt_by_time, digits = 3, caption = "Between-species Wilcoxon by time (Shannon)")

Table 8: Between-species Wilcoxon by time (Shannon)

Time	med_CAU	med_CYM	p
T0	5.188	4.927	0.081
T1	5.198	5.056	0.383
T2	5.207	5.080	0.173

bt_overall_p

## [1] 0.01300303

The overall Wilcoxon test indicated a species effect across time points (report printed bt_overall_p). By-time Wilcoxon tests (unadjusted p-values as printed in the table) suggest a marginal difference at T0, with higher diversity in Caulerpa, whereas differences at T1 and T2 were not statistically significant. Taken together, the figure and tests indicate that Caulerpa generally sustains higher Shannon diversity than Cymodocea, while temporal dynamics—especially the T0→T1 increase in Cymodocea and the slight T1→T2 softening under heatwave—are modest in magnitude.

3.0.1 Acclimation change (T0 → T1) within species

We next examined acclimation effects by directly comparing Shannon diversity between T0 and T1 for each species.

acclim <- datos %>%
  group_by(Species) %>%
  summarise(
    med_T0 = median(shanon[Time == "T0"], na.rm = TRUE),
    med_T1 = median(shanon[Time == "T1"], na.rm = TRUE),
    p = {
      x <- shanon[Time == "T0"]; y <- shanon[Time == "T1"]
      if (length(x) > 0 && length(y) > 0)
        suppressWarnings(stats::wilcox.test(x, y, exact = FALSE)$p.value)
      else NA_real_
    },
    direction = case_when(med_T1 > med_T0 ~ "increase",
                          med_T1 < med_T0 ~ "decrease",
                          TRUE            ~ "no_change"),
    .groups = "drop"
  )

kable(acclim, digits = 3, caption = "T0 vs T1 (acclimation) by species")

Table 9: T0 vs T1 (acclimation) by species

Species	med_T0	med_T1	p	direction
CAU	5.188	5.198	0.663	increase
CYM	4.927	5.056	0.383	increase

During the acclimation period (T0 → T1), Shannon diversity showed a slight increase in both Caulerpa and Cymodocea sediments (median values rising from 5.19 to 5.20 and from 4.93 to 5.06, respectively). However, these changes were not statistically significant (p = 0.66 for Caulerpa, p = 0.38 for Cymodocea), indicating that although diversity tended to rise during acclimation, the magnitude of the increase was modest and within the range of sampling variability.

3.1 Temporal change under Control (T0–T1–T2)

To assess whether Shannon diversity varied over time in the absence of heatwave stress, we applied Kruskal–Wallis tests separately for Caulerpa and Cymodocea under control conditions. This approach evaluates overall differences across the three sampling times (T0, T1, T2) without assuming normality.

datos <- read_table("cell_shanon_data_12_05_25_complete.txt") %>% 
  mutate(
    Species   = factor(Species),
    Time      = factor(Time, levels = c("T0","T1","T2")),
    Treatment = factor(Treatment),
    cells     = as.numeric(cells)
  )

kw_ctrl <- datos %>%
  filter(Treatment == "Control") %>%
  group_by(Species) %>%
  summarise(
    kw_p = {
      d <- cur_data()
      suppressWarnings(kruskal.test(shanon ~ Time, data = d)$p.value)
    },
    .groups = "drop"
  )

kable(kw_ctrl, digits = 3, caption = "Kruskal–Wallis test across T0–T1–T2 under control conditions (by species)")

Table 10: Kruskal–Wallis test across T0–T1–T2 under control conditions (by species)

Species	kw_p
CAU	0.733
CYM	0.432

The results (Table) show no significant temporal variation in Shannon diversity under control conditions (p = 0.733 for Caulerpa, p = 0.432 for Cymodocea). This indicates that, in the absence of heatwave exposure, microbial diversity remained relatively stable across the course of the experiment in both host species.

3.2 Temporal change under Heatwave (T0- T1–T2)

To evaluate whether heatwave exposure altered the temporal trajectory of Shannon diversity, we applied Kruskal–Wallis tests across the three time points within each species.

kw_hw <- datos %>%
  filter(Treatment == "HW") %>%
  group_by(Species) %>%
  summarise(
    kw_p = {
      d <- cur_data()
      suppressWarnings(kruskal.test(shanon ~ Time, data = d)$p.value)
    },
    .groups = "drop"
  )

kable(kw_hw, digits = 3, caption = "Kruskal–Wallis across T0–T1–T2 under heatwave conditions (by species)")

Table 11: Kruskal–Wallis across T0–T1–T2 under heatwave conditions (by species)

Species	kw_p
CAU	0.875
CYM	0.288

Under heatwave conditions, no significant temporal changes were detected in either species (Caulerpa: p = 0.875; Cymodocea: p = 0.288). These results indicate that, while the figure suggests a slight T1→T2 softening in Cymodocea under heatwave exposure, the magnitude of the shift was insufficient to reach statistical significance. Combined with the control analysis, this supports the view that Shannon diversity remained broadly stable over time in both species, with only modest, non-significant fluctuations under heat stress.

3.3 Caulerpa control averages between T1 and T2

To probe short-interval changes under control conditions, we compared Shannon diversity between T1 and T2 for Caulerpa using descriptive summaries and a Wilcoxon test as a robust alternative to the Welch t-test.

target_var <- "shanon"

dat <- datos %>%
  filter(Species == "CAU", Treatment == "Control", Time %in% c("T1","T2")) %>%
  select(ID = dplyr::any_of("ID"), Time, value = all_of(target_var)) %>%
  filter(!is.na(value))

summary_tbl <- dat %>%
  group_by(Time) %>%
  summarise(
    n    = dplyr::n(),
    mean = mean(value),
    sd   = sd(value),
    se   = sd/sqrt(n),
    .groups = "drop"
  )

knitr::kable(summary_tbl, digits = 3,
             caption = "Caulerpa — Control: comparison of Shannon diversity between T1 and T2 (mean, SD, SE, n)")

Table 12: Caulerpa — Control: comparison of Shannon diversity between T1 and T2 (mean, SD, SE, n)

Time	n	mean	sd	se
T1	3	5.202	0.075	0.043
T2	3	5.195	0.047	0.027

tt_welch <- t.test(value ~ Time, data = dat, var.equal = FALSE)
tt_welch

## 
##  Welch Two Sample t-test
## 
## data:  value by Time
## t = 0.13793, df = 3.353, p-value = 0.8982
## alternative hypothesis: true difference in means between group T1 and group T2 is not equal to 0
## 95 percent confidence interval:
##  -0.1453022  0.1593022
## sample estimates:
## mean in group T1 mean in group T2 
##         5.201667         5.194667

w_test <- stats::wilcox.test(value ~ Time, data = dat, exact = FALSE)
w_test

## 
##  Wilcoxon rank sum test with continuity correction
## 
## data:  value by Time
## W = 5, p-value = 1
## alternative hypothesis: true location shift is not equal to 0

The summary table shows nearly identical means at T1 and T2 (5.202 vs 5.195), with small standard errors. Welch’s test confirmed no evidence of a difference (t = 0.138, df = 3.35, p = 0.898; 95% CI for the mean difference: −0.145 to 0.159). Results were consistent with the Welch test, showing no evidence of a difference between time points (Wilcoxon p = 1). Given the very small sample size (n = 3 per time), these findings should be interpreted as compatible with negligible change rather than proof of no effect. Thus, Shannon diversity in Caulerpa remained stable between T1 and T2 under control conditions.

3.4 Caulerpa heatwave averages between T1 and T2

To check short-interval changes under heatwave conditions, we compared Shannon diversity between T1 and T2 for Caulerpa using descriptive summaries and a Wilcoxon test as a robust alternative to the Welch t-test.

dat <- datos %>%
  filter(Species == "CAU", Treatment == "HW", Time %in% c("T1","T2")) %>%
  select(ID = dplyr::any_of("ID"), Time, value = all_of(target_var)) %>%
  filter(!is.na(value))

summary_tbl <- dat %>%
  group_by(Time) %>%
  summarise(
    n    = dplyr::n(),
    mean = mean(value),
    sd   = sd(value),
    se   = sd/sqrt(n),
    .groups = "drop"
  )

knitr::kable(summary_tbl, digits = 3,
             caption = "Caulerpa – HW: T1 vs T2 (mean, SD, n)")

Table 13: Caulerpa – HW: T1 vs T2 (mean, SD, n)

Time	n	mean	sd	se
T1	3	5.202	0.075	0.043
T2	3	5.180	0.139	0.080

tt_welch <- t.test(value ~ Time, data = dat, var.equal = FALSE)
tt_welch

## 
##  Welch Two Sample t-test
## 
## data:  value by Time
## t = 0.23467, df = 3.0672, p-value = 0.8293
## alternative hypothesis: true difference in means between group T1 and group T2 is not equal to 0
## 95 percent confidence interval:
##  -0.2644285  0.3070952
## sample estimates:
## mean in group T1 mean in group T2 
##         5.201667         5.180333

w_test <- stats::wilcox.test(value ~ Time, data = dat, exact = FALSE)
w_test

## 
##  Wilcoxon rank sum test with continuity correction
## 
## data:  value by Time
## W = 4, p-value = 1
## alternative hypothesis: true location shift is not equal to 0

The summary table shows very similar means at T1 and T2 (5.202 vs 5.180) with small standard errors. Both Welch’s test (t = 0.235, df = 3.07, p = 0.829; 95% CI for the mean difference: –0.264 to 0.308) and the Wilcoxon rank-sum test (W = 4, p = 1.00) indicated no evidence of a difference between the two time points. Thus, under heatwave conditions, Caulerpa diversity remained essentially stable between T1 and T2. Given the small sample size (n = 3 per time), these results should be interpreted as consistent with a negligible effect rather than proof of no effect.

3.5 Cymodocea control averages between T1 and T2

dat <- datos %>%
  filter(Species == "CYM", Treatment == "Control", Time %in% c("T1","T2")) %>%
  select(ID = dplyr::any_of("ID"), Time, value = all_of(target_var)) %>%
  filter(!is.na(value))

summary_tbl <- dat %>%
  group_by(Time) %>%
  summarise(
    n    = dplyr::n(),
    mean = mean(value),
    sd   = sd(value),
    se   = sd/sqrt(n),
    .groups = "drop"
  )

knitr::kable(summary_tbl, digits = 3,
             caption = "Cymodocea – Control: T1 vs T2 (mean, SD, n)")

Table 14: Cymodocea – Control: T1 vs T2 (mean, SD, n)

Time	n	mean	sd	se
T1	3	5.073	0.165	0.095
T2	3	5.084	0.203	0.117

tt_welch <- t.test(value ~ Time, data = dat, var.equal = FALSE)
tt_welch

## 
##  Welch Two Sample t-test
## 
## data:  value by Time
## t = -0.077316, df = 3.8365, p-value = 0.9422
## alternative hypothesis: true difference in means between group T1 and group T2 is not equal to 0
## 95 percent confidence interval:
##  -0.4377554  0.4144221
## sample estimates:
## mean in group T1 mean in group T2 
##         5.072667         5.084333

w_test <- stats::wilcox.test(value ~ Time, data = dat, exact = FALSE)
w_test

## 
##  Wilcoxon rank sum test with continuity correction
## 
## data:  value by Time
## W = 4.5, p-value = 1
## alternative hypothesis: true location shift is not equal to 0

The summary statistics indicate that Cymodocea maintained very similar Shannon diversity values between T1 (mean = 5.073, SE = 0.095) and T2 (mean = 5.084, SE = 0.117). Both Welch’s two-sample t-test (t = –0.077, df = 3.84, p = 0.942) and the Wilcoxon rank-sum test (W = 5, p = 1.00) confirmed the absence of significant differences between the two time points. These findings suggest that under control conditions, Cymodocea diversity remained stable across the short interval from T1 to T2, with no detectable changes despite minor variation in the group means.

3.6 Cymodocea heatwave averages between T1 and T2

dat <- datos %>%
  filter(Species == "CYM", Treatment == "HW", Time %in% c("T1","T2")) %>%
  select(ID = dplyr::any_of("ID"), Time, value = all_of(target_var)) %>%
  filter(!is.na(value))

summary_tbl <- dat %>%
  group_by(Time) %>%
  summarise(
    n    = dplyr::n(),
    mean = mean(value),
    sd   = sd(value),
    se   = sd/sqrt(n),
    .groups = "drop"
  )

knitr::kable(summary_tbl, digits = 3,
             caption = "Cymodocea – HW: T1 vs T2 (mean, SD, n)")

Table 15: Cymodocea – HW: T1 vs T2 (mean, SD, n)

Time	n	mean	sd	se
T1	3	5.073	0.165	0.095
T2	3	5.056	0.106	0.061

tt_welch <- t.test(value ~ Time, data = dat, var.equal = FALSE)
tt_welch

## 
##  Welch Two Sample t-test
## 
## data:  value by Time
## t = 0.14762, df = 3.4062, p-value = 0.891
## alternative hypothesis: true difference in means between group T1 and group T2 is not equal to 0
## 95 percent confidence interval:
##  -0.3195780  0.3529113
## sample estimates:
## mean in group T1 mean in group T2 
##         5.072667         5.056000

w_test <- stats::wilcox.test(value ~ Time, data = dat, exact = FALSE)
w_test

## 
##  Wilcoxon rank sum test with continuity correction
## 
## data:  value by Time
## W = 4, p-value = 1
## alternative hypothesis: true location shift is not equal to 0

The descriptive statistics for Cymodocea under heatwave conditions show nearly identical Shannon diversity means at T1 (5.073, SE = 0.095) and T2 (5.056, SE = 0.061). Welch’s two-sample t-test found no evidence of a difference (t = 0.148, df = 3.41, p = 0.891; 95% CI: –0.320 to 0.352), and the Wilcoxon rank-sum test likewise indicated no shift in location (W = 5, p = 1.00).

4 Taxa biodiversity analysis

Datos.Muestras=data.frame(read_excel("TablaOTUs.xlsx"))
Samples.original=Datos.Muestras$ID 
DF.0.original=Datos.Muestras[,-c(1,2)]
row.names(DF.0.original)=Samples.original
OTUs=paste("OTU",1:dim(DF.0.original)[2],sep="")
names(DF.0.original)=OTUs

Sizes=rowSums(DF.0.original)

Tipos.original=as.factor(rep(c("CAU_T0","CAU_T1","CAU_T2C", "CAU_T2HW","CYM_T0","CYM_T1", "CYM_T2C","CYM_T2HW"),each=3))

4.1 Comparison of Shannon indices indices of sample types

We have quantified the biodiversity of every type of samples CAU_T* or CYM_T* by means of the Shannon index of the sample obtained by merging the 3 samples of that type. To test which pairs of sample types had significantly different Shannon indices, we have used the Hutcheson t-test, as implemented in function Hutcheson_t_test of the R package ecolTest, and adjusted the p-values with the Holm method.

# Shannon index
SH=function(x){
  vegan::diversity(x,index = "shannon")
}

p.lnp2=function(p){
  if (p==0){return(0)}
  else {
    return(p*(log(p)^2))
  }
}

# Hutcheson variance estimator
Var.SH=function(x){
N=sum(x)
y=sapply(x/sum(x),FUN=p.lnp2)
bit=sapply(x,FUN=function(x){min(x,1)})
S=sum(bit)
vv=(sum(y)-SH(x)^2)/N+(S-1)/(2*N^2)
return(vv)
}

# Standard deviation estimator
sd.SH=function(x){
  sqrt(Var.SH(x))
}

Samples=Samples.original
DF.0=DF.0.original
Tipos=Tipos.original
DF.0.agrup=aggregate(DF.0,by=list(Tipos),FUN=sum)[,-1]

For each sample, we compute its Shannon index and an estimation of its standard deviation (sd):

Resultados=data.frame(Samples,
round(apply(DF.0,MARGIN=1,SH),4),
round(apply(DF.0,MARGIN=1,sd.SH),4))
row.names(Resultados)=NULL
names(Resultados)=c("Samples","SH","sd")

flextable(Resultados)|>
   fontsize(size = 8, part = "all")|>
 width(width = 0.9) 

Samples	SH	sd
CAU_T0_1	5.2297	0.0099
CAU_T0_2	5.0583	0.0083
CAU_T0_3	5.1884	0.0108
CAU_T1_1	5.2781	0.0098
CAU_T1_2	5.1297	0.0099
CAU_T1_3	5.1981	0.0104
CAU_T2C_1	5.1477	0.0102
CAU_T2C_2	5.1980	0.0096
CAU_T2C_3	5.2405	0.0109
CAU_T2HW_1	5.2974	0.0072
CAU_T2HW_2	5.0278	0.0085
CAU_T2HW_3	5.2167	0.0078
CYM_T0_1	4.8018	0.0083
CYM_T0_2	4.9936	0.0098
CYM_T0_3	4.9272	0.0081
CYM_T1_1	4.9171	0.0052
CYM_T1_2	5.0564	0.0056
CYM_T1_3	5.2460	0.0065
CYM_T2C_1	5.3003	0.0063
CYM_T2C_2	5.0557	0.0063
CYM_T2C_3	4.8975	0.0066
CYM_T2HW_1	4.9353	0.0067
CYM_T2HW_2	5.1045	0.0064
CYM_T2HW_3	5.1299	0.0066

The next graphic depicts, for each sample, its Shannon index \(SH\) and the error bar \(SH\pm 2\cdot sd\).

row.names(Resultados)=Samples

plot(0.1*(1:24),Resultados$SH,
     col=rep(c(rep("green",3),rep("blue",3),rep("purple",3),rep("red",3)),2), 
     pch=c(rep(20,12),rep(18,12)),cex=1,
     xlab="",ylab="Shannon index",xaxt='n',
     main="All samples")
legend("bottomleft",col=c("black","black","green","blue","purple","red"),
       pch=c(20,18,NA,NA,NA,NA),
       lty=c(NA,NA,1,1,1,1),
       legend=c("CAU","CYM","T0","T1","T2C","T2HW"),
       seg.len=0.5,cex=0.5)
segments(0.1*(1:24),Resultados$SH-2*Resultados$sd,
         0.1*(1:24),Resultados$SH+2*Resultados$sd,
         col=rep(c(rep("green",3),rep("blue",3),rep("purple",3),rep("red",3)),2),lwd=1.5)

We repeat the process for sample types: for each sample type, we merge all three samples of that type into a single sample. We include the intervals (SH-3·sd,SH+3·sd). The reason for the factor 3 is that there are 36 pairs of samples to compare, and hence we use as factor for sd the 0.95^1/36 quantile of the standard normal distribution. In this way, disjoint intervals give statistical evidence (at the 5% signification level) that the corresponding two indices are different.

Resultados.agrupados=data.frame(levels(Tipos),
round(apply(DF.0.agrup,MARGIN=1,SH),4),
round(apply(DF.0.agrup,MARGIN=1,sd.SH),4),
round(apply(DF.0.agrup,MARGIN=1,SH)-3*apply(DF.0.agrup,MARGIN=1,sd.SH),4),
round(apply(DF.0.agrup,MARGIN=1,SH)+3*apply(DF.0.agrup,MARGIN=1,sd.SH),4)
)
row.names(Resultados.agrupados)=NULL
names(Resultados.agrupados)=c("Samples","SH","sd","SH-3sd","SH+3sd")

flextable(Resultados.agrupados)|>
   fontsize(size = 8, part = "all")|>
 width(width = 0.9) 

Samples	SH	sd	SH-3sd	SH+3sd
CAU_T0	5.2009	0.0056	5.1842	5.2176
CAU_T1	5.2607	0.0059	5.2428	5.2785
CAU_T2C	5.2590	0.0060	5.2410	5.2770
CAU_T2HW	5.2457	0.0046	5.2319	5.2594
CYM_T0	4.9321	0.0051	4.9168	4.9474
CYM_T1	5.1190	0.0034	5.1089	5.1291
CYM_T2C	5.1226	0.0038	5.1113	5.1338
CYM_T2HW	5.0875	0.0039	5.0759	5.0991

plot(0.1*(1:8),Resultados.agrupados$SH,col=rep(c("green","blue","purple","red"),2),
     pch=c(rep(20,4),rep(18,4)),
     xlab="",ylab="Shannon index",xaxt='n',
     main="All sample types")
segments(0.1*(1:8),Resultados.agrupados$SH-3*Resultados.agrupados$sd,
         0.1*(1:8),Resultados.agrupados$SH+3*Resultados.agrupados$sd,
         col=rep(c("green","blue","purple","red"),2),lwd=1.5)
legend("bottomleft",col=c("black","black","green","blue","purple","red"),
       pch=c(20,18,NA,NA,NA,NA),
       lty=c(NA,NA,1,1,1,1),
      legend=c("CAU","CYM","T0","T1","T2C","T2HW"),
       seg.len=0.5,cex=0.5)

SH indices of CAU samples are significantly different from (and actually significantly larger than) those of CYM samples.

plot(0.1*(1:4),Resultados.agrupados$SH[1:4],col=c("green","blue","purple","red"),
     pch=20,main="CAU sample types",
     xlab="",ylab="Shannon index",xaxt='n',
     ylim=c(min(Resultados.agrupados$SH[1:4]-3*Resultados.agrupados$sd[1:4]),
              max(Resultados.agrupados$SH[1:4]+3*Resultados.agrupados$sd[1:4])))
segments(0.1*(1:4),Resultados.agrupados$SH[1:4]-3*Resultados.agrupados$sd[1:4],
         0.1*(1:4),Resultados.agrupados$SH[1:4]+3*Resultados.agrupados$sd[1:4],
         col=c("green","blue","purple","red"),lwd=1.5)
legend("topright",col=c("green","blue","purple","red"),
       pch=20,legend=c("T0","T1","T2C","T2HW"),seg.len=0.5,cex=0.5)

Only the SH index of T0 samples seems to be significantly different from the others.

plot(0.1*(1:4),Resultados.agrupados$SH[5:8],col=c("green","blue","purple","red"),
     pch=18,main="CYM sample types",
     xlab="",ylab="Shannon index",xaxt='n',          ylim=c(min(Resultados.agrupados$SH[5:8]-3*Resultados.agrupados$sd[5:8]),max(Resultados.agrupados$SH[5:8]+3*Resultados.agrupados$sd[5:8])))
segments(0.1*(1:4),Resultados.agrupados$SH[5:8]-3*Resultados.agrupados$sd[5:8],
         0.1*(1:4),Resultados.agrupados$SH[5:8]+3*Resultados.agrupados$sd[5:8],
         col=c("green","blue","purple","red"),lwd=1.5)
legend("topleft",col=c("green","blue","purple","red"),
       pch=18,legend=c("T0","T1","T2C","T2HW"),seg.len=0.5,cex=0.5)

All four SH indices are significantly different, except for T1 and T2C.

We can use Hutcheson t-test to decide whether Shannon indices are significantly different. We perform pairwise comparisons and adjust the p-values using the Holm method. The conclusions are the same.

pvalSH.G=matrix(NA,nrow=8,ncol=8)
for (i in 1:7){
  for (j in (i+1):8){
   pvalSH.G[i,j]= Hutcheson_t_test(DF.0.agrup[i,],DF.0.agrup[j,])$p.value
  }
}
pvalSH.G=matrix(p.adjust(pvalSH.G,method="holm"),nrow=8)

colnames(pvalSH.G)=levels(Tipos)
row.names(pvalSH.G)=levels(Tipos)

flextable(data.frame(round(pvalSH.G,6)))|>
   fontsize(size = 8, part = "all")|>
 width(width = 0.9) 

CAU_T0	CAU_T1	CAU_T2C	CAU_T2HW	CYM_T0	CYM_T1	CYM_T2C	CYM_T2HW
	0	0.000000	0.000000	0	0	0.000000	0
		0.950346	0.179925	0	0	0.000000	0
			0.228577	0	0	0.000000	0
				0	0	0.000000	0
					0	0.000000	0
						0.950346	0
							0

4.2 Behaviour of Shannon indices under thresholds

We address the following question: If we set a threshold \(p_0\), we only retain from each sample the OTUs that appear with a relative frequency \(\geqslant p_0\) and calculate the Shannon index (SH) of those samples, how does its longitudinal behavior vary from T0->T1->T2C->T2HW as \(p_0\) increases?

We use the following method to answer this question:

• We consider \(p_0\) thresholds from 0.00005 (0.005%) to 0.05 (5%), advancing in steps of 0.00005.
• For each threshold, in each sample, we retain the OTUs whose relative frequency is \(\geqslant p_0\)
• Then, we group the samples by sample type and compute the SH of the grouped samples.
• We visually analyze the trend in SH among CAU and CYM samples as \(p_0\) increases.
• We also compute, for each type of sample and for relevant thresholds, the proportion of OTUs present in at least one sample of that type whose relative frequency in all three samples of that type is greater than or equal to the threshold.

We obtain that, in the CAU samples, at some point between the 0.15% and 0.2% thresholds, and in the CYM samples, at some point between the 0.1% and 0.15% thresholds, the longitudinal behavior of the SH changes for the first time from that observed in the whole samples, shifting from a rise-fall-fall pattern to a rise-fall-rise pattern.

For each type of CAU sample, around 12-13% of OTUs present in at least one sample of this type have relative frequency in all three samples of that type greater than or equal to 0.1%. For CYM sample types, this figure descends to 9-10%.

# threshold
llindar=function(x,l){
if (x>=l){return(1)}
  else{return(0)}
}

#Global sample
DF.0=as.matrix(DF.0)
DF.0.prop=DF.0/rowSums(DF.0)
DF.0.agrup=as.matrix(DF.0.agrup)
DF.0.agrup.prop=DF.0.agrup/rowSums(DF.0.agrup)

Original sample sizes and range of proportions within them:

Tamaños=rowSums(DF.0)
Props.min=round(apply(DF.0.prop,MARGIN=1,function(x){min(x[x>0])}),6)
Props.max=apply(DF.0.prop,MARGIN=1,function(x){max(x[x>0])})
Info=data.frame(Tamaños,Props.min,Props.max)
names(Info)=c("Size","Smallest prop.","Largest prop.")

flextable(Info)|>
   fontsize(size = 8, part = "all")|>
 width(width = 0.9) 

Size	Smallest prop.	Largest prop.
32452	0.000031	0.05805497
45161	0.000022	0.05832466
26298	0.000038	0.05354019
31355	0.000032	0.05243183
30592	0.000033	0.05458944
29368	0.000034	0.07147235
30554	0.000033	0.05194083
33119	0.000030	0.05694616
26568	0.000038	0.06884222
62616	0.000016	0.06188514
43726	0.000023	0.06026163
50715	0.000020	0.05223307
57062	0.000018	0.10017174
38684	0.000026	0.09365629
56482	0.000018	0.09686272
145523	0.000007	0.11633900
122687	0.000008	0.08515980
82489	0.000012	0.08112597
91168	0.000011	0.06932257
97111	0.000010	0.09009278
97125	0.000010	0.12887516
88157	0.000011	0.14189457
94560	0.000011	0.11748096
89922	0.000011	0.11695692

4.2.1 Original sample

Resultados.Agrupados=data.frame(
  SH=apply(DF.0.agrup,MARGIN=1,SH),
  Varianza=apply(DF.0.agrup,MARGIN=1,Var.SH))

##
plot(0.1*(1:8),Resultados.Agrupados$SH,col=rep(c("green","blue","purple","red"),2),
     pch=c(rep(20,4),rep(18,4)),
     xlab="",ylab="SH",xaxt='n',
     main="Grouped samples")
segments(0.1*(1:8),Resultados.Agrupados$SH-3*sqrt(Resultados.Agrupados$Varianza),
         0.1*(1:8),Resultados.Agrupados$SH+3*sqrt(Resultados.Agrupados$Varianza),
         col=rep(c("green","blue","purple","red"),2),lwd=1.5)
legend("topright",col=c("black","black","green","blue","purple","red"),
       pch=c(20,18,NA,NA,NA,NA),
       lty=c(NA,NA,1,1,1,1),
      legend=c("CAU","CYM","T0","T1","T2C","T2HW"),
       seg.len=0.5,cex=0.5)

#
plot(0.1*(1:4),Resultados.Agrupados$SH[1:4],col=c("green","blue","purple","red"),
     pch=20,main="Grouped samples: CAU",
     xlab="",ylab="SH",xaxt='n',
     ylim=c(min(Resultados.Agrupados$SH[1:4]-3*sqrt(Resultados.Agrupados$Varianza[1:4])),
              max(Resultados.Agrupados$SH[1:4]+3*sqrt(Resultados.Agrupados$Varianza[1:4]))))
segments(0.1*(1:4),Resultados.Agrupados$SH[1:4]-3*sqrt(Resultados.Agrupados$Varianza[1:4]),
         0.1*(1:4),Resultados.Agrupados$SH[1:4]+3*sqrt(Resultados.Agrupados$Varianza[1:4]),
         col=c("green","blue","purple","red"),lwd=1.5)
legend("topleft",col=c("green","blue","purple","red"),
       pch=20,legend=c("T0","T1","T2C","T2HW"),cex=0.5)

#
plot(0.1*(1:4),Resultados.Agrupados$SH[5:8],col=c("green","blue","purple","red"),
     pch=18,main="Grouped samples: CYM",
     xlab="",ylab="SH",xaxt='n',          ylim=c(min(Resultados.Agrupados$SH[5:8]-3*sqrt(Resultados.Agrupados$Varianza[5:8])),max(Resultados.Agrupados$SH[5:8]+3*sqrt(Resultados.Agrupados$Varianza[5:8]))))
segments(0.1*(1:4),Resultados.Agrupados$SH[5:8]-3*sqrt(Resultados.Agrupados$Varianza[5:8]),
         0.1*(1:4),Resultados.Agrupados$SH[5:8]+3*sqrt(Resultados.Agrupados$Varianza[5:8]),
         col=c("green","blue","purple","red"),lwd=1.5)
legend("topleft",col=c("green","blue","purple","red"),
       pch=18,legend=c("T0","T1","T2C","T2HW"),cex=0.5)

4.2.2 Enter thresholds

Resultados=c()
for (i in 1:1000){
print(i)
i0=i*0.00005
llindar.0=function(x){llindar(x,i0)}
DD=vapply(DF.0.prop, llindar.0, numeric(1))*DF.0
DD.agrup=aggregate(DD,by=list(Tipos),FUN=sum)[,-1]
Resultados=rbind(Resultados,
       c(apply(DD.agrup,MARGIN=1,SH),#Shannon
       apply(DD.agrup,MARGIN=1,sd.SH),#Variança
       apply(DD.agrup,MARGIN=1,SH)-3*apply(DD.agrup,MARGIN=1,sd.SH), #LE de l'IC
       apply(DD.agrup,MARGIN=1,SH)+3*apply(DD.agrup,MARGIN=1,sd.SH),#UE  de l'IC
       
       i0 #llindar
       ))
}


Resultados=data.frame(Resultados)

names(Resultados)=c(paste("SH",levels(Tipos),sep="."),
      paste("sd",levels(Tipos),sep="."),
      paste("LE",levels(Tipos),sep="."),
      paste("UE",levels(Tipos),sep="."),
      "threshold")

saveRDS(Resultados, file="Resultados.Shannon.Umbrales.RData")

p.valores=c()
for (i in 1:1000){
print(i)
i0=i*0.00005
llindar.0=function(x){llindar(x,i0)}
DD=vapply(DF.0.prop, llindar.0, numeric(1))*DF.0
DD.agrup=aggregate(DD,by=list(Tipos),FUN=sum)[,-1]


pvalSH.G=matrix(NA,nrow=8,ncol=8)
for (i in 1:7){
  for (j in (i+1):8){
   pvalSH.G[i,j]= Hutcheson_t_test(DD.agrup[i,],DD.agrup[j,])$p.value
  }
}
pvalSH.G=p.adjust(pvalSH.G,method="holm")

p.valores=rbind(p.valores,
                c(i0,
                  pvalSH.G))

}

write.csv(p.valores, file="p.valores.Shannon.Umbrales.csv",row.names=FALSE)

The results are in the file “Resultados.Shannon.Umbrales.RData”. Its variables are (for each type of sample: CAU_T0, CAU_T1 etc.):

• SH.type: The Shannon index (SH) of the union of the three samples of that type

• sd.type: The estimated standard deviation of the SH of the union of the three samples of that type

• LE.type: SH minus 3 times the estimated standard deviation

• UE.type: SH plus 3 times the estimated standard deviation

• Threshold: The corresponding threshold

We show its first 10 rows (rounded, and splitted into different tables, for horizontal space reasons), corresponding to thresholds from 0.00005 to 0.0005. :

Resultados=readRDS("Resultados.Shannon.Umbrales.RData")
names(Resultados)=c(paste("SH",levels(Tipos),sep="."),
      paste("sd",levels(Tipos),sep="."),
      paste("LE",levels(Tipos),sep="."),
      paste("UE",levels(Tipos),sep="."),
      "Threshold")

Resultados.r4=Resultados
Resultados.r4[,1:32]=round(Resultados.r4[,1:32],4)

flextable(Resultados.r4[1:10,c(33,1+8*(0:3),2+8*(0:3))])|>
   fontsize(size = 8, part = "all")|>
 width(width = 0.9) 

Threshold	SH.CAU_T0	sd.CAU_T0	LE.CAU_T0	UE.CAU_T0	SH.CAU_T1	sd.CAU_T1	LE.CAU_T1	UE.CAU_T1
0.00005	5.1252	0.0053	5.1092	5.1412	5.1997	0.0058	5.1824	5.2170
0.00010	5.0481	0.0051	5.0326	5.0635	5.1092	0.0055	5.0926	5.1257
0.00015	5.0011	0.0050	4.9859	5.0162	5.0479	0.0054	5.0318	5.0641
0.00020	4.9245	0.0049	4.9098	4.9391	4.9787	0.0052	4.9630	4.9944
0.00025	4.8751	0.0048	4.8607	4.8895	4.9337	0.0052	4.9182	4.9491
0.00030	4.8395	0.0047	4.8253	4.8537	4.8735	0.0050	4.8584	4.8887
0.00035	4.7807	0.0046	4.7668	4.7946	4.8427	0.0050	4.8277	4.8577
0.00040	4.7456	0.0046	4.7319	4.7594	4.8042	0.0049	4.7893	4.8190
0.00045	4.7104	0.0045	4.6968	4.7239	4.7588	0.0049	4.7442	4.7733
0.00050	4.6612	0.0044	4.6479	4.6745	4.7291	0.0048	4.7146	4.7435

flextable(Resultados.r4[1:10,c(33,3+8*(0:3),4+8*(0:3))])|>
   fontsize(size = 8, part = "all")|>
 width(width = 0.9) 

Threshold	SH.CAU_T2C	sd.CAU_T2C	LE.CAU_T2C	UE.CAU_T2C	SH.CAU_T2HW	sd.CAU_T2HW	LE.CAU_T2HW	UE.CAU_T2HW
0.00005	5.1943	0.0058	5.1769	5.2117	5.1539	0.0043	5.1408	5.1669
0.00010	5.1027	0.0056	5.0860	5.1194	5.0714	0.0042	5.0588	5.0839
0.00015	5.0536	0.0055	5.0372	5.0699	5.0186	0.0041	5.0063	5.0309
0.00020	4.9697	0.0053	4.9539	4.9855	4.9529	0.0040	4.9409	4.9649
0.00025	4.9234	0.0052	4.9078	4.9389	4.9069	0.0039	4.8952	4.9187
0.00030	4.8896	0.0051	4.8743	4.9050	4.8537	0.0038	4.8422	4.8653
0.00035	4.8425	0.0050	4.8274	4.8576	4.8159	0.0038	4.8045	4.8274
0.00040	4.8079	0.0050	4.7929	4.8228	4.7660	0.0037	4.7548	4.7772
0.00045	4.7851	0.0050	4.7702	4.7999	4.7365	0.0037	4.7254	4.7476
0.00050	4.7406	0.0049	4.7259	4.7553	4.7040	0.0037	4.6930	4.7150

flextable(Resultados.r4[1:10,c(33,5+8*(0:3),6+8*(0:3))])|>
   fontsize(size = 8, part = "all")|>
 width(width = 0.9) 

Threshold	SH.CYM_T0	sd.CYM_T0	LE.CYM_T0	UE.CYM_T0	SH.CYM_T1	sd.CYM_T1	LE.CYM_T1	UE.CYM_T1
0.00005	4.8502	0.0049	4.8355	4.8649	5.0004	0.0032	4.9909	5.0100
0.00010	4.7581	0.0047	4.7440	4.7722	4.9137	0.0031	4.9045	4.9229
0.00015	4.6853	0.0046	4.6717	4.6990	4.8593	0.0030	4.8503	4.8684
0.00020	4.6284	0.0045	4.6149	4.6418	4.7987	0.0030	4.7898	4.8075
0.00025	4.5794	0.0044	4.5662	4.5927	4.7475	0.0029	4.7387	4.7562
0.00030	4.5353	0.0044	4.5222	4.5483	4.7035	0.0029	4.6948	4.7121
0.00035	4.5003	0.0043	4.4874	4.5132	4.6659	0.0029	4.6573	4.6745
0.00040	4.4627	0.0043	4.4499	4.4754	4.6107	0.0028	4.6023	4.6191
0.00045	4.4162	0.0042	4.4036	4.4288	4.5693	0.0028	4.5609	4.5776
0.00050	4.3812	0.0042	4.3687	4.3937	4.5383	0.0028	4.5300	4.5466

flextable(Resultados.r4[1:10,c(33,7+8*(0:3),8+8*(0:3))])|>
   fontsize(size = 8, part = "all")|>
 width(width = 0.9) 

Threshold	SH.CYM_T2C	sd.CYM_T2C	LE.CYM_T2C	UE.CYM_T2C	SH.CYM_T2HW	sd.CYM_T2HW	LE.CYM_T2HW	UE.CYM_T2HW
0.00005	5.0126	0.0036	5.0019	5.0233	4.9765	0.0037	4.9655	4.9875
0.00010	4.9095	0.0034	4.8992	4.9197	4.8922	0.0036	4.8816	4.9029
0.00015	4.8446	0.0033	4.8346	4.8546	4.8148	0.0035	4.8044	4.8252
0.00020	4.7855	0.0033	4.7756	4.7953	4.7597	0.0034	4.7494	4.7699
0.00025	4.7292	0.0032	4.7195	4.7388	4.7049	0.0034	4.6948	4.7150
0.00030	4.6798	0.0032	4.6702	4.6893	4.6562	0.0033	4.6462	4.6661
0.00035	4.6419	0.0032	4.6324	4.6513	4.6095	0.0033	4.5997	4.6193
0.00040	4.5895	0.0031	4.5802	4.5988	4.5639	0.0032	4.5542	4.5736
0.00045	4.5482	0.0031	4.5390	4.5575	4.5322	0.0032	4.5226	4.5418
0.00050	4.5203	0.0030	4.5111	4.5294	4.5011	0.0032	4.4915	4.5106

We start by checking several thresholds:

• 0.0001: OTUs that represent more than 0.01% in their samples
• 0.001: OTUs that represent more than 0.1% in their samples
• 0.0025: OTUs that represent more than 0.25% in their samples
• 0.005: OTUs that represent more than 0.5% in their samples
• 0.0075: OTUs that represent more than 0.75% in their samples
• 0.01: OTUs that represent more than 1% in their samples
• 0.025: OTUs that represent more than 2.5% in their samples

Dibu.global=function(p){
  Tall=as.matrix(Resultados[Resultados$Threshold==p,])
plot(0.1*(1:8),Tall[1,1:8],
     col=rep(c("green","blue","purple","red"),2),
     pch=c(rep(20,4),rep(18,4)),
     xlab="",ylab="SH",xaxt='n',main=paste("Threshold",p,sep=" "))
segments(x0=0.1*(1:8),y0=Tall[1,17:24],
         x1=0.1*(1:8),y1=Tall[1,25:32],
         col=rep(c("green","blue","purple","red"),2),lwd=1.5)
legend("topright",col=c("black","black","green","blue","purple","red"),
       pch=c(20,18,NA,NA,NA,NA),
       lty=c(NA,NA,1,1,1,1),
      legend=c("CAU","CYM","T0","T1","T2C","T2HW"),
       seg.len=0.5,cex=0.5)
}

Dibu.global(0.0001)

Dibu.global(0.001)

Dibu.global(0.0025)

Dibu.global(0.005)

Dibu.global("0.0075")

Dibu.global(0.01)

Dibu.global(0.025)

As it can be seen, the longitudinal behavior of Shannon indices changes from p₀=0.1% (which is similar to the global behaviour) to 0.25%.

Let us see the graphics for thresholds between 0.001 and 0.005:

for (i in 0:8){
Dibu.global(0.001+0.0005*i)
}

4.2.3 How many OTUs are we talking about?

For each type of samples, the next graph represents the proportion of OTUs present in at least one sample of this type whose relative frequency in all three samples of that type is greater than or equal to the percentage indicated on the x-axis. The proportions are also given in a table.

  n=seq(from=0.001,to=0.003,by=0.0005)
  N=length(n)
Result=n
for (i in 1:8){
 X1=DF.0.prop[3*(i-1)+1,]
 X1=sort(X1[X1!=0])
 X2=DF.0.prop[3*(i-1)+2,]
 X2=sort(X2[X2!=0])
 X3=DF.0.prop[3*(i-1)+3,]
 X3=sort(X3[X3!=0])

  PP=rep(0,N)
  for(j in 1:N){PP[j]=length(X1[X1>=n[j]] & X2[X2>=n[j]] & X3[X3>=n[j]])/length(X1[X1>0] | X2[X2>0] | X3[X3>0])}
  plot(100*n,PP,pch=20,type="l",lwd=1.5,xaxp=c(0.1,0.3,N),yaxp=c(0,0.2,20),xlab="%",ylab="Proportion of OTUs whose percentage is higher than ...",main=Tipos[i])
  abline(v=0.01*(0:100),lwd=0.5,col="red")
  abline(h=0.01*(0:100),lwd=0.5,col="red")
  abline(v=0.15,lwd=1,col="blue")
 Result=cbind(Result,round(PP,4)) 
}

Result=data.frame(Result)
names(Result)=c("Threshold",levels(Tipos))
row.names(Result)=NULL


flextable(Result)|>
   fontsize(size = 8, part = "all")|>
 width(width = 0.9) 

Threshold	CAU_T0	CAU_T1	CAU_T2C	CAU_T2HW	CYM_T0	CYM_T1	CYM_T2C	CYM_T2HW
0.0010	0.1269	0.1283	0.1394	0.1162	0.1027	0.0896	0.0922	0.0901
0.0015	0.0968	0.0929	0.1004	0.0829	0.0759	0.0662	0.0643	0.0683
0.0020	0.0751	0.0765	0.0797	0.0652	0.0610	0.0508	0.0539	0.0550
0.0025	0.0609	0.0650	0.0632	0.0546	0.0521	0.0388	0.0446	0.0459
0.0030	0.0509	0.0526	0.0563	0.0446	0.0417	0.0342	0.0348	0.0363

5 Samples divergence analysis

According to the Bray-Curtis distance (correctly applied to compositions), the CAU and CYM samples at T0 are more different than at T1, more similar at T1 than at T2C, and again more similar at T2HW than at T2C (or than at T1 or T0, for that matter). Overall, the global sets of CAU and CYM samples are more different than the starting T0 samples, as if part of the original differences were diluted. Are these differences statistically significant?

Well, we have devised a method to assess the statistical significance of the differences in median distances between two pairs of samples groups, based on a resampling procedure. Using this method, we obtain that these convergences and divergences from T0 to T1, from T1 to T2C, from T2C to T2HW, and from T0 to the global sample, are statistically significant.

DF.0.agrup=aggregate(DF.0,by=list(Tipos),FUN=sum)[,-1]

The next table shows, for each level T0, T1, T2C, T2HW, and Global (all samples), the median Bray-Curtis (BC) distances between the compositions of the CAU and CYM samples at those levels.

Times	Average BC-dist.
T0	0.4124
T1	0.4097
T2C	0.4493
T2HW	0.3766
Global	0.4189

The BC-distances decrease from T0 to T1. Then, from T1 to T2C they increase, while from T1 to T2HW they decrease further. Also, from T0 to Global it decreases. Are these “convergences” and “divergences” of samples statistically significant?

We want to perform a contrast with null hypothesis “The CAU_T1 and CYM_T1 samples are as similar as the CAU_T0 and CYM_T0 samples” and alternative hypothesis “The CAU_T1 and CYM_T1 samples are more similar than the CAU_T0 and CYM_T0 samples”.

To solve this contrast, we resort to a resampling process. The broad idea is:

• On the one hand, we merge all 3 samples CAU_T0 in a single sample, and all 3 samples CYM_T0 in another single sample, and we repeat 1000 times the following:

  • We split the CAU merged sample into 3 disjoint random samples of the sizes of the original CAU_T0_1, CAU_T0_2, CAU_T0_3 samples forming it
  • We split the CYM merged sample into 3 disjoint random samples of the sizes of the original CYM_T0_1, CYM_T0_2, CYM_T0_3 samples forming it
  • We compute the median distance between the 3 CAU random samples and the 3 CYM random samples

  In this way, we obtain a vector of 1000 median distances between CAU and CYM for T0

• On the other hand, we merge all 6 samples CAU_T0 and CAU_T1 in a single sample, and all 6 samples CYM_T0 and CYM_T1 in another single sample, and we repeat 1000 times the following:

  • We take from the CAU merged sample 3 disjoint random samples (without reposition) of the sizes of the original CAU_T0_1, CAU_T0_2, CAU_T0_3 samples
  • We take from the CYM merged sample into 3 disjoint random samples (without reposition) of the sizes of the original CYM_T0_1, CYM_T0_2, CYM_T0_3 samples
  • We compute the median distance between the 3 CAU random samples and the 3 CYM random samples

  In this way, we obtain a vector of 1000 median distances between CAU and CYM for the union of T0 and T1

The idea is that if the T1 samples are “as similar” as the T0 samples, the median distances between triples of disjoint random samples from the merged T0 samples should be similar to the median distances between triples of disjoint random samples (of the same sizes) from the merged T0+T1 samples. Conversely, if the T1 samples are “more similar” than the T0 samples, the median distances between triples of random samples from the merged T0 samples should tend to be larger than the median distances between triples of random samples (of the same sizes) from the merged T0+T1 samples.

So, we can use as p-value the proportion of pairs (median distance between CAU and CYM for T0, median distance between CAU and CYM for T0+T1) where the first entry is smaller than the second entry. If the T1 samples are “as similar” as the T0 samples, we would expect this to happen half of times, while if the T0 samples are more different than the T1 samples, we would expect this to happen with low frequency.

The problem is that the CYM samples are larger than CAU samples, and it can bias the samples; for instance if we merge CAU_T1 and CYM_T1 samples and take random samples, most of the taxa will come from CYM:

Samples	Sizes
CAU_T0_1	32452
CAU_T0_2	45161
CAU_T0_3	26298
CAU_T1_1	31355
CAU_T1_2	30592
CAU_T1_3	29368
CYM_T0_1	57062
CYM_T0_2	38684
CYM_T0_3	56482
CYM_T1_1	145523
CYM_T1_2	122687
CYM_T1_3	82489

To solve this drawback, and since we apply BC-distances to proportions, we reescale all samples to size 10⁶ (up to rounding; we need integer frequencies for the simulations) before merging.

DF=round(DF.0.prop*10^6)
DF.prop=DF/rowSums(DF)
DF.agrup=aggregate(DF,by=list(Tipos),FUN=sum)[,-1]
Sizes=rowSums(DF)

The new sample sizes are

Samples	Sizes
CAU_T0_1	1000070
CAU_T0_2	999907
CAU_T0_3	999911
CAU_T1_1	1000070
CAU_T1_2	1000030
CAU_T1_3	999912
CYM_T0_1	1000234
CYM_T0_2	1000111
CYM_T0_3	1000043
CYM_T1_1	1000078
CYM_T1_2	999876
CYM_T1_3	999852

Let us check first that with these reescaled samples (where, due to rounding, the proportions are not exactly the original ones but very close to them), the behaviour of the distances is the same as the original one:

Times	Average BC-dist.
T0	0.4124
T1	0.4097
T2C	0.4493
T2HW	0.3766
Global	0.4189

No change.

We shall use the following function:

• Function Simulation
  • takes the different samples CAU y CYM at the specified times, for instance, CAU_T0, CAU_T1, CYM_T0 and CYM_T1, or simply CAU_T0 and CYM_T0
  • considers as “base” samples the samples CAU and CYM at the first of each set of times, for instance CAU_T0 and CYM_T0
  • merges all samples CAU in one sample, and all samples CYM in another sample
  • it extracts, from the CAU merged sample, 3 disjoint random samples (without reposition) of the same sizes as the reescaled CAU base samples, and from the CYM merged sample, 3 disjoint random samples of the same sizes as the reescaled CYM base samples
  • it computes the median specified distance between the 3 CAU random samples and the 3 CYM random samples

#' II indexes of the CAU grouped samples
#' The first one is the "base" time
#' Example: CAU T0+T1 and CYM T0+T1 vs CAU T0 and CYM T0
#' II=c(1,2)
#' Example: CAU_T0 vs CYM_T0
#' II=c(1)
Simulation=function(II,distancia){
#CAU
XX1=c()
for (i in 1:length(II)){
  XX1=c(XX1,rep(OTUs,DF.agrup[II[i],]))
}
XX1=factor(XX1,levels=OTUs)
ind1=1:length(XX1)
#CYM
XX2=c()
for (i in 1:length(II)){
  XX2=c(XX2,rep(OTUs,DF.agrup[4+II[i],]))
}
XX2=factor(XX2,levels=OTUs)
ind2=1:length(XX2)

# sizes of base samples
SS=Sizes[c(3*(II[1]-1)+1:3,3*((4+II[1])-1)+1:3)]


ind1.1=sample(ind1,SS[1],replace=FALSE)
ind1.2=sample(ind1[-ind1.1],SS[2],replace=FALSE)
ind1.3=sample(ind1[-c(ind1.1,ind1.2)],SS[3],replace=FALSE)

ind2.1=sample(ind2,SS[4],replace=FALSE)
ind2.2=sample(ind2[-ind2.1],SS[5],replace=FALSE)
ind2.3=sample(ind2[-c(ind2.1,ind1.2)],SS[6],replace=FALSE)

Y1.1=prop.table(table(factor(XX1[ind1.1],levels=OTUs)))
Y1.2=prop.table(table(factor(XX1[ind1.2],levels=OTUs)))
Y1.3=prop.table(table(factor(XX1[ind1.3],levels=OTUs)))
Y2.1=prop.table(table(factor(XX2[ind2.1],levels=OTUs)))
Y2.2=prop.table(table(factor(XX2[ind2.2],levels=OTUs)))
Y2.3=prop.table(table(factor(XX2[ind2.3],levels=OTUs)))

YY=rbind(Y1.1,Y1.2,Y1.3,Y2.1,Y2.2,Y2.3)

BC=c()
for (i in 1:3){
  for (j in 4:6){
    BC=c(BC,vegan::vegdist(YY[c(i,j),], method=distancia))
  }
}
median(BC)
}

For reproducibility, we fix a random seed

#initial_seed=as.integer(Sys.time())
#print(initial_seed)
## [1] 1725986963
#initial_seed%%10000
## [1] 6963

set.seed(6963)

Let us perform the desired contrast for T0 vs T1 and the BC-distance

Sim.T0T1.T0.BC=replicate(1000,Simulation(c(1,2),"bray"))
Sim.T0.BC=replicate(1000,Simulation(c(1),"bray"))

saveRDS(Sim.T0T1.T0.BC, file="Sim.T0T1.T0.BC.RData")
saveRDS(Sim.T0.BC, file="Sim.T0.BC.RData")

The median BC-distances for the random T0+T1 samples go from 0.3877 to 0.3895, while the median BC-distances for the T0 samples go from 0.4057 to 0.407. So, all median BC-distances for T0 are larger than any median distance for T0+T1. Moreover, recall that the median BC-distance between the (reescaled) CAU_T0 and CYM_T0 samples was 0.4124, larger than the largest median BC-distance for the random T0+T1 samples.

For robustness, let us perform the contrast with T1 as base samples

Sim.T0T1.T1.BC=replicate(1000,Simulation(c(2,1),"bray"))
Sim.T1.BC=replicate(1000,Simulation(c(2),"bray"))

saveRDS(Sim.T0T1.T1.BC, file="Sim.T0T1.T1.BC.RData")
saveRDS(Sim.T1.BC, file="Sim.T1.BC.RData")

In this case, the median BC-distances for the T0+T1 samples go from 0.3874 to 0.3894, while the median BC-distances for the T1 samples go from 0.3792 to 0.3807. The median BC-distance between the (reescaled) CAU_T1 and CYM_T1 samples was 0.4097.

Now T1 vs T2C, taking T1 as base samples (for the sake of completeness, we repeat the simulation for T1).

Sim.T1T2C.T1.BC=replicate(1000,Simulation(c(2,3),"bray"))
Sim.T1.BC.2=replicate(1000,Simulation(c(2),"bray"))

saveRDS(Sim.T1T2C.T1.BC, file="Sim.T1T2C.T1.BC.RData")
saveRDS(Sim.T1.BC.2, file="Sim.T1.BC.2.RData")

The median BC-distances for the T1+T2C samples go from 0.3971 to 0.3994, while the median BC-distances for the T1 samples go from 0.3792 to 0.3806. The median BC-distance between the (reescaled) CAU_T1 and CYM_T1 samples was 0.4097.

And T2C vs T2HW, with T2C as base samples.

Sim.T2CT2HW.T2C.BC=replicate(1000,Simulation(c(3,4),"bray"))
Sim.T2C.BC=replicate(1000,Simulation(c(3),"bray"))

saveRDS(Sim.T2CT2HW.T2C.BC,file="Sim.T2CT2HW.T2C.BC.RData")
saveRDS(Sim.T2C.BC, file="Sim.T2C.BC.RData")

The median BC-distances for the T2C+T2HW samples go from 0.385 to 0.3869, while the median BC-distances for the T2C samples go from 0.4274 to 0.4288. The median BC-distance between the (reescaled) CAU_T2C and CYM_T2C samples was 0.4493

Finally, the global samples:

Sim.Global.BC=replicate(1000,Simulation(c(1,2,3,4),"bray"))
Sim.T0.BC=replicate(1000,Simulation(c(1),"bray"))

saveRDS(Sim.Global.BC, file="Sim.Global.BC.RData")
saveRDS(Sim.T0.BC, file="Sim.T0.BC.RData")

The median BC-distances bewteen CAU and CYM for the Global samples go from 0.3805 to 0.3828, while the median BC-distances for the T0 samples go from 0.4057 to 0.407. The median BC-distance between the (reescaled) CAU_T0 and CYM_T0 samples was 0.4124

6 Differential abundance analysis

For each pair of sample types considered, we proceed as follows:

1. We load TablaOTUs.xlsx and retain only the relevant “global” samples (all, only CAU, or only CYM).
   

2. We remove OTUs with 2 or fewer reads across the selected samples.
   

3. We remove OTUs that appear in only one of the selected samples, in order to apply Bayesian-multiplicative zero imputation.
   

4. We perform Bayesian-multiplicative zero imputation on the selected samples.

5. We retain only the samples corresponding to the time points to be compared.

6. We assess whether and how well the two types of samples are clearly separated in a hierarchical clustering.
   

7. We study how well the two types of samples separate when only a random group of OTUs of fixed size is considered, for different sizes. This provides a reference against which we evaluate the significance of the separation observed with specific groups of OTUs.

   To evaluate how a group of taxa separates two groups of samples CAU_x and CYM_x, we use the index
   \[ \frac{\text{distance between CAU${}_x$ and CYM${}_x$}}{\sqrt{(\text{dist. within CAU${}_x$})^2 + (\text{dist. within CYM${}_x$})^2}} \]
   where the distances are calculated as the heights in the hierarchical tree obtained by clustering the samples with the selected taxa.

   In each one of these simulations, we fix the random seed as the last four digits of Sys.time() at the moment of execution.

8. We search for groups of OTUs with significantly different abundances in the two sample types by applying several methods: significance according to ALDeX (adjusted p-values from the Kruskal–Wallis test); relevant log-ratios; bacterial signatures identified with coda_glmnet; and significance according to simper.
   

9. When the different methods identify groups of OTUs that consistently separate the two sample types, we record them in a table Significant, and finally we export this table as a csv file. Its name is “OTU_Significativos_” followed by the pair of sample types.

6.1 CAU vs CYM

tax_otu=data.frame(read_excel("TablaOTUs.xlsx"))
Samples=tax_otu$ID 
n.OTUs.original=dim(tax_otu)[2]-2
taxa=colnames(tax_otu[,3:dim(tax_otu)[2]])
DF.0=tax_otu[,-c(1,2)]
taxa.original=taxa
OTUs=paste("OTU",1:n.OTUs.original,sep="")
colnames(DF.0)=OTUs
DF.0.total=DF.0
colnames(DF.0.total)=OTUs
rownames(DF.0.total)=Samples
rm(tax_otu)

Type=as.factor(rep(c("CAU","CYM"),each=12))
colors=c("green","blue")[Type]
#' Green: CAU  
#' Blue: CYM  

The OTUs that appear with 2 or fewer hits in the total sample represent 15.8% of the total.

Miseria=as.vector(which(colSums(DF.0)<=2))
DF.0=DF.0[,-Miseria]
taxa=taxa[-Miseria]
OTUs=OTUs[-Miseria]

# DF.0.hits: para cada OTU y cada muestra, 1 si OTU in Muestra y 0 si no
hit=function(x){min(c(x,1))}
DF.0.hits=as.matrix(DF.0)
DF.0.hits[]=vapply(DF.0.hits, hit, numeric(1))

OTUs that appear in only one sample but represent more than 0.05% of that sample:

Unics=data.frame(
Sample=rep(NA,length(which(colSums(DF.0.hits)==1))), OTUs=names(colSums(DF.0)[which(colSums(DF.0.hits)==1)]), Reads=colSums(DF.0)[which(colSums(DF.0.hits)==1)],
            Proportions=rep(0,length(which(colSums(DF.0.hits)==1)))  
)
for (i in 1:length(Unics$OTUs)){
ii=which(DF.0.hits[,Unics$OTUs[i]]==1)  
Unics$Proportions[i]=DF.0[ii,Unics$OTUs[i]]/sum(DF.0[ii,])
Unics$Sample[i]=Samples[ii]}
Unics.Freqs=Unics[Unics$Proportions>=0.05/100,]
row.names(Unics.Freqs)=NULL


Unics.Freqs[rev(order(Unics.Freqs$Proportions)),] %>%
  kbl() %>%
  kable_styling()

Sample	OTUs	Reads	Proportions
CAU_T0_2	OTU966	55	0.0012183

We remove the OTUs that appear in only one samples and we perform Bayesian-multiplicative zero imputation.

DF.0=DF.0[,-which(colSums(DF.0.hits)==1)]
taxa=taxa[-which(colSums(DF.0.hits)==1)]
OTUs=OTUs[-which(colSums(DF.0.hits)==1)]
row.names(DF.0)=Samples
DF=zCompositions::cmultRepl(DF.0,method="GBM",output="p-counts",suppress.print=TRUE,z.warning=0.99)
row.names(DF)=Samples

rm(DF.0.hits)
rm(Miseria)

From 3088 initial taxa, we have reduced to 2542.

6.1.1 How different are the samples?

HC=ClusterHC(DF,Grups=Type,barplot=FALSE,colores=colors)

separacio.global=Sep(HC)

The two sample types are perfectly separated from the start. The separation between groups is 2.47.

We observe below that the two sample types are so different that almost any subset of OTUs of reasonable size classifies them correctly. This will serve as a reference to compare how much improvement we gain with the “good” sets identified later.

> initial_seed=as.integer(Sys.time())
> print (initial_seed)
# [1] 1711395644
initial_seed %% 10000
# [1] 5644

set.seed(5644)
Experimento=function(i)
{
  ii=sample(dim(DF)[2],i,rep=FALSE)
  DFtemp=DF[,ii]
  CC=ClusterHC(DFtemp,dendrograma=FALSE,barplot=FALSE, Grups=Type,colores=colors)
  c(Encerts(CC$tabla,table(Type)),Sep(CC))
}
n=250
F.SS=c()
for (i in 10:round((dim(DF)[2])/2))
  {
  print(i)
  EE=replicate(n,Experimento(i))
  EE.2=EE[2,which(EE[1,]==0)]
XX=replicate(1000,mean(sample(EE.2,n,replace=TRUE)))
  F.SS=rbind(F.SS, c(i,
                     length(EE.2)/250,
                      mean(EE.2),
                      quantile(XX,0.025),
                      quantile(XX,0.975)
  ))
  }
colnames(F.SS)=c("n","Proportion","Avg. sep.","Q_0.025","Q_0.975")
saveRDS(F.SS, file="Fraccio.Separadors.CAUvsCYM.RData")

F.SS=readRDS("Fraccio.Separadors.CAUvsCYM.RData")

The first plot shows, for each \(n\) up to half the total number of OTUs, the proportion of samples of size \(n\) that perfectly classify CAU and CYM (black curve), along with the 95% Clopper–Pearson confidence interval for that proportion (red curves). We have used smoothing splines to smooth the curves.

F.SS_prop.Q_0.025=epitools::binom.exact(F.SS[,2]*250,250)$lower
F.SS_prop.Q_0.975=epitools::binom.exact(F.SS[,2]*250,250)$upper
fit = smooth.spline(F.SS[,1],F.SS[,2],cv=TRUE)
fit.low = smooth.spline(F.SS[,1],F.SS_prop.Q_0.025,cv=TRUE)
fit.up = smooth.spline(F.SS[,1],F.SS_prop.Q_0.975,cv=TRUE)


plot(F.SS[,1:2],pch=20,cex=0.25,col="darkgrey",xlab="n",ylab="Proportion",main="Proportion of perfect classifiers",xlim=c(0,1250),xaxp=c(0,1250,25),yaxp=c(0,1,10))
lines(fit,col="black",lwd=1)
lines(fit.low,col="red",lwd=1)
lines(fit.up,col="red",lwd=1)

The second plot shows, for each \(n\) up to half the total number of OTUs, the estimated mean separation obtained with a sample of size \(n\) that perfectly classifies CAU and CYM (black curve), along with the 95% confidence interval of this mean separation obtained via bootstrap (red curve). This plot will serve as a reference later.

fit = smooth.spline(F.SS[,1],F.SS[,3],cv=TRUE)
fit.low = smooth.spline(F.SS[,1],F.SS[,4],cv=TRUE)
fit.up = smooth.spline(F.SS[,1],F.SS[,5],cv=TRUE)

plot(F.SS[,c(1,3)],pch=20,cex=0.25,col="darkgrey",xlab="n",ylab="Separation",main="Average separation for perfect classifiers",xlim=c(0,1250),xaxp=c(0,1250,25),yaxp=c(0,2.5,10))
lines(fit,col="black",lwd=1)
lines(fit.low,col="red",lwd=1)
lines(fit.up,col="red",lwd=1)
abline(h=separacio.global,col="green")

`

6.1.2 OTUs significant according to ALDeX

We always use the aldexCesc.clr version of the aldex.clr function (from the script funcionsCODAMETACIRCLE.R) to generate the simulated samples.

> initial_seed=as.integer(Sys.time())
> print (initial_seed)
# [1] 1711411362
initial_seed %% 10000
# [1] 1362

set.seed(1362)
repl.kw.Cescv2.CaCy=aldexCesc.clr(t(DF), conds=Type, mc.samples=1000, verbose=FALSE)
aldex.kw.Cescv2.CaCy=aldex.kw(repl.kw.Cescv2.CaCy, verbose=FALSE)
#'
saveRDS(aldex.kw.Cescv2.CaCy, file="aldex_kw_Cescv2_CaCy.RData")

p.valores_kw=readRDS("aldex_kw_Cescv2_CaCy.RData") 

Adjusted Kruskal–Wallis p-value < 0.05

sep.kw.005=QQ.HC.noadjust(p.valores_kw,DF,Type,q=0.05,1)

kw.005=which(p.valores_kw[,2]<0.05) 

There are 804 taxa with adjusted Kruskal–Wallis p-value < 0.05.
The separation between groups is 2.48.

Adjusted Kruskal–Wallis p-value < 0.01

sep.kw.001=QQ.HC.noadjust(p.valores_kw,DF,Type,q=0.01,1)

kw.001=which(p.valores_kw[,2]<0.01) 

There are 605 taxa with adjusted Kruskal–Wallis p-value < 0.01.
The separation between groups is 2.35.

Adjusted Kruskal–Wallis p-value < 0.001

sep.kw.0001=QQ.HC.noadjust(p.valores_kw,DF,Type,q=0.001,1)

kw.0001=which(p.valores_kw[,2]<0.001) 

There are 408 taxa with adjusted Kruskal–Wallis p-value < 0.001.
The separation between groups is 2.89.

Indicador=function(x,k=n.OTUs.original){
  xx=rep(0,k)
  y=as.numeric(gsub("\\D+", "", OTUs[x]))
  xx[y]=1
  
  return(xx)
}

Significant=data.frame(
  OTUs=paste("OTU",1:n.OTUs.original,sep=""),
  taxa=taxa.original,
  Aldex.kw.0.05=Indicador(kw.005),
  Aldex.kw.0.01=Indicador(kw.001),
  Aldex.kw.0.001=Indicador(kw.0001)
  )

6.1.3 Taxa with maximum relevant log-ratios

We plot the assoc_k values (see the main text) and obtain its maximum.

LRS=explore_logratios(DF,Type)
saveRDS(LRS, file="LRS_CAUCYM.RData")

LRS=readRDS("LRS_CAUCYM.RData")

assoc=rep(0,dim(DF)[2]-4)
for (m in 5:dim(DF)[2]){
    assoc[m-4]=sum(LRS$`association log-ratio with y`[1:m,1:m])/m^2
}
saveRDS(assoc, file="assoc_CAUCYM.RData")

assoc=readRDS("assoc_CAUCYM.RData")
plot(5:dim(DF)[2],assoc,type="b",xlab="m",ylab="Average goodness of the m most logratio-relevant taxa."
     ,pch=20,cex=0.5)

m=4+which.max(assoc)
impLR=sort(as.numeric(LRS$`order of importance`[1:m]))
DF.Imp=DF[,impLR]
HC=ClusterHC(DF.Imp,dendrograma=FALSE,barplot=FALSE, Grups=Type)
LR.max=c(length(impLR),Sep(HC))

The maximum is attained at the set of 103 most logratio-relevant taxa.
They perfectly separate the two sample types. The separation between groups is 6.58.

Significant=cbind(Significant,
                     Log_ratio.max=Indicador(impLR))

6.1.4 Taxa relevant for the bacterial signature (according to coda_glmnet)

We always apply the coda_glmnet function to the frequency matrix with zeros already imputed.

coda.glmnet=coda_glmnet(DF,Type,showPlots = FALSE)
saveRDS(coda.glmnet, file="coda.glmnet.CAUCYM.RData")

coda.glmnet=readRDS("coda.glmnet.CAUCYM.RData")
coda.glmnet$`signature plot`

impGLMNET=coda.glmnet$taxa.num
DF.Imp=DF[,impGLMNET]
HC=ClusterHC(DF.Imp,dendrograma=TRUE,barplot=FALSE,Grups=Type,colores=colors)

SB.glmnet=c(length(coda.glmnet$taxa.num),Sep(HC))

There are 118 significant taxa.
The separation between groups is 4.55.

Significant=cbind(Significant,
glmnet_sign.CAU=Indicador(coda.glmnet$taxa.num[coda.glmnet$`log-contrast coefficients`>0]),
glmnet_sign.CYM=Indicador(coda.glmnet$taxa.num[coda.glmnet$`log-contrast coefficients`<0]))

6.2 Simper

We always use simper from vegan on the (original) proportion matrix.

DF.prop=DF.0.total/rowSums(DF.0.total)
SMP.prop=simper(DF.prop,group=Type)

indexos_SMP.rel.prop=SMP.prop$CAU_CYM$ord[which(SMP.prop$CAU_CYM$cusum<=0.7)]
OTUs.simper.rel.prop=sort(attr(SMP.prop$CAU_CYM$cusum[which(SMP.prop$CAU_CYM$cusum<=0.7)],"names"))

DF.Imp=DF[,OTUs.simper.rel.prop]
HC=ClusterHC(DF.Imp,dendrograma=TRUE,barplot=FALSE,Grups=Type,colores=colors)

simper.rel.props=c(length(indexos_SMP.rel.prop),Sep(HC))

There are 93 significant taxa. They perfectly separate the two sample types. The separation between groups is 2.88.

Indicador.Gl=function(x,k=n.OTUs.original){
  xx=rep(0,k)
 xx[x]=1
  return(xx)
}

Significant=cbind(Significant,
simper.props=Indicador.Gl(indexos_SMP.rel.prop))

Significant=cbind(Significant,
t(DF.prop))

6.2.1 Summary

write.csv2(Significant,"OTU_Significativos_CAUvsCYM_def.csv",row.names=FALSE)

Resultados=rbind(
sep.kw.0001,sep.kw.005,sep.kw.001,
LR.max,SB.glmnet,
simper.rel.props
)
row.names(Resultados)=c("Aldex.0.001","Aldex.0.05","Aldex.0.01",
"LR","glmnet", "simper")
colnames(Resultados)=c("Size","Separation")

par(opar)
fit = smooth.spline(F.SS[,1],F.SS[,3],cv=TRUE)
fit.low = smooth.spline(F.SS[,1],F.SS[,4],cv=TRUE)
fit.up = smooth.spline(F.SS[,1],F.SS[,5],cv=TRUE)

plot(F.SS[,c(1,3)],pch=20,cex=0.25,col="darkgrey",xlab="n",ylab="Separation",main="Average separation for perfect classifiers",xaxp=c(0,1000,40),yaxp=c(0,8.5,17),ylim=c(0,8.5),xlim=c(0,1000))
lines(fit,col="black",lwd=1)
lines(fit.low,col="red",lwd=1)
lines(fit.up,col="red",lwd=1)
points(Resultados,col="blue",type="h")
points(Resultados,col="blue",pch=20)
text(Resultados[,1],Resultados[,2]+0.1,col="blue",labels=row.names(Resultados),cex=0.75)
abline(h=2.47,col="green")
text(20,2.6,col="green",labels="Global",cex=0.75)

Finally, we intersect the OTUs identified as significant according to LR and coda_glmnet.

Significant.capat=Significant[,c(1,2,6,7,8)]
Significant.capat=cbind(Significant.capat,Cuánto=rowSums(Significant.capat[,3:dim(Significant.capat)[2]]))
Significant.capat=Significant.capat[Significant.capat$Cuánto==2,]

There are 41 such taxa. They are

Significant.capat[,1:2]%>%
  kbl() %>%
  kable_styling()

	OTUs	taxa
OTU22	OTU22	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfobacterales.f__Desulfosarcinaceae.g__Desulfatitalea.s__uncultured_Desulfobacteraceae
OTU30	OTU30	d__Bacteria.p__Bacteroidota.c__Ignavibacteria.o__Ignavibacteriales.f__PHOS.HE36.g__PHOS.HE36.s__uncultured_bacterium
OTU32	OTU32	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfobacterales.f__Desulfosarcinaceae.guncultured.
OTU35	OTU35	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfobacterales.f__Desulfosarcinaceae.g__LCP.80.s__uncultured_delta
OTU38	OTU38	Unassigned.__.....__
OTU39	OTU39	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Sphingobacteriales.f__Lentimicrobiaceae.g__Lentimicrobiaceae.s__uncultured_Bacteroidetes
OTU42	OTU42	d__Bacteria.p__Myxococcota.c__Polyangia.o__Polyangiales.f__Sandaracinaceae.guncultured.
OTU45	OTU45	d__Bacteria.p__Desulfobacterota.c__Desulfobulbia.o__Desulfobulbales.f__Desulfocapsaceae..
OTU46	OTU46	d__Bacteria.p__Bacteroidota.c__Ignavibacteria.o__Ignavibacteriales.f__Ignavibacteriaceae.gIgnavibacterium.
OTU70	OTU70	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.oDesulfobacterales...
OTU109	OTU109	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfobacterales.f__Desulfosarcinaceae.gLCP.80.
OTU133	OTU133	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfatiglandales.f__Desulfatiglandaceae.gDesulfatiglans.
OTU141	OTU141	d__Bacteria.p__Bdellovibrionota.c__Oligoflexia.o__0319.6G20.f__0319.6G20.g0319.6G20.
OTU213	OTU213	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfobacterales.f__Desulfosarcinaceae.gDesulfatitalea.
OTU218	OTU218	d__Bacteria.p__Spirochaetota.c__Leptospirae.o__Leptospirales.f__Leptospiraceae.g__RBG.16.49.21.s__uncultured_organism
OTU223	OTU223	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Sphingobacteriales.f__ST.12K33.g__ST.12K33.s__uncultured_Cytophagales
OTU229	OTU229	d__Bacteria.p__Spirochaetota.c__Leptospirae.o__Leptospirales.f__Leptospiraceae.g__RBG.16.49.21.s__uncultured_bacterium
OTU230	OTU230	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Cytophagales.f__Cyclobacteriaceae.g__uncultured.s__uncultured_Bacteroidetes
OTU253	OTU253	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfatiglandales.f__Desulfatiglandaceae.g__Desulfatiglans.s__uncultured_delta
OTU255	OTU255	d__Bacteria.p__Spirochaetota.c__V2072.189E03.o__V2072.189E03.f__V2072.189E03.g__V2072.189E03.s__uncultured_organism
OTU256	OTU256	d__Bacteria.p__Fermentibacterota.c__Fermentibacteria.o__Fermentibacterales.f__Fermentibacteraceae.g__Fermentibacteraceae.s__uncultured_bacterium
OTU269	OTU269	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Chromatiales.f__Chromatiaceae.gCandidatus_Thiobios.
OTU451	OTU451	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Flavobacteriales.f__Flavobacteriaceae.gActibacter.
OTU498	OTU498	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfatiglandales.f__Desulfatiglandaceae.g__Desulfatiglans.s__uncultured_organism
OTU527	OTU527	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfobacterales.f__Desulfobacteraceae.g__Desulfotignum.s__uncultured_bacterium
OTU761	OTU761	d__Bacteria.p__Actinobacteriota.c__Acidimicrobiia.o__Microtrichales.f__Microtrichaceae.gSva0996_marine_group.
OTU811	OTU811	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfobacterales.f__Desulfosarcinaceae.g__Desulfosarcina.s__uncultured_bacterium
OTU881	OTU881	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Thiotrichales.f__Thiotrichaceae.g__uncultured.s__uncultured_gamma
OTU890	OTU890	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Flavobacteriales.f__Flavobacteriaceae.g__Robiginitalea.s__uncultured_Bacteroidetes
OTU1107	OTU1107	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfobacterales.f__Desulfosarcinaceae.g__Sva0081_sediment_group.s__metagenome
OTU1329	OTU1329	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfobacterales.f__Desulfococcaceae.gDesulfonema.
OTU1390	OTU1390	d__Bacteria.p__Gemmatimonadota.c__PAUC43f_marine_benthic_group.o__PAUC43f_marine_benthic_group.f__PAUC43f_marine_benthic_group.g__PAUC43f_marine_benthic_group.s__saltmarsh_clone
OTU1419	OTU1419	d__Bacteria.p__NB1.j.c__NB1.j.o__NB1.j.f__NB1.j.g__NB1.j.s__uncultured_bacterium
OTU1443	OTU1443	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__B2M28.f__B2M28.g__B2M28.s__uncultured_proteobacterium
OTU1461	OTU1461	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Flavobacteriales.f__Flavobacteriaceae.g__Robiginitalea.s__Robiginitalea_myxolifaciens
OTU1532	OTU1532	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Chromatiales.f__Chromatiaceae.g__Candidatus_Thiobios.s__uncultured_organism
OTU1594	OTU1594	d__Bacteria.p__Bacteroidota.c__Ignavibacteria.o__Ignavibacteriales.f__PHOS.HE36.gPHOS.HE36.
OTU1701	OTU1701	d__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Rhizobiales.f__Methyloligellaceae.gMethyloceanibacter.
OTU1839	OTU1839	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Ectothiorhodospirales.f__Thioalkalispiraceae.g__Thioalkalispira.Sulfurivermis.s__uncultured_Thioalkalispiraceae
OTU2338	OTU2338	d__Bacteria.p__Cyanobacteria.c__Cyanobacteriia.o__Cyanobacteriales.f__Xenococcaceae.gXenococcus_PCC.7305.
OTU2371	OTU2371	d__Bacteria.p__Firmicutes.c__Clostridia.o__Lachnospirales.f__Lachnospiraceae.gRoseburia.

DF.Imp=DF[,Significant.capat[,1]]
HC=ClusterHC(DF.Imp,dendrograma=TRUE,barplot=FALSE,Grups=Type,colores=colors)

The separation between groups is 7.86.

We update the plot with the separations:

intersección=c(dim(Significant.capat)[1],Sep(HC))
Resultados=rbind(Resultados,intersección)
row.names(Resultados)=c("Aldex.0.001","Aldex.0.05","Aldex.0.01",
"LR","glmnet", "simper","intersection")
colnames(Resultados)=c("Size","Separation")

par(opar)
fit = smooth.spline(F.SS[,1],F.SS[,3],cv=TRUE)
fit.low = smooth.spline(F.SS[,1],F.SS[,4],cv=TRUE)
fit.up = smooth.spline(F.SS[,1],F.SS[,5],cv=TRUE)

plot(F.SS[,c(1,3)],pch=20,cex=0.25,col="darkgrey",xlab="n",ylab="Separation",main="Average separation for perfect classifiers",xaxp=c(0,1000,40),yaxp=c(0,8.5,17),ylim=c(0,8.5),xlim=c(0,1000))
lines(fit,col="black",lwd=1)
lines(fit.low,col="red",lwd=1)
lines(fit.up,col="red",lwd=1)
points(Resultados,col="blue",type="h")
points(Resultados,col="blue",pch=20)
text(Resultados[,1],Resultados[,2]+0.1,col="blue",labels=row.names(Resultados),cex=0.75)
abline(h=2.47,col="green")
text(20,2.6,col="green",labels="Global",cex=0.75)

Resultados %>%
  kbl() %>%
  kable_styling()

	Size	Separation
Aldex.0.001	408	2.889614
Aldex.0.05	804	2.481799
Aldex.0.01	605	2.354071
LR	103	6.579296
glmnet	118	4.550477
simper	93	2.881239
intersection	41	7.863271

6.3 CAU T0 vs CYM T0

tax_otu=data.frame(read_excel("TablaOTUs.xlsx"))
Samples=tax_otu$ID 
taxa=colnames(tax_otu[,3:dim(tax_otu)[2]])
OTUs=paste("OTU",1:(dim(tax_otu)[2]-2),sep="")


DF.0=tax_otu[c(1:3,13:15),-c(1,2)]
row.names(DF.0)=Samples[c(1:3,13:15)]
colnames(DF.0)=OTUs

taxa.original=taxa
DF.0.original=DF.0
n.OTUs.original=dim(DF.0)[2]

Miseria=as.vector(which(colSums(DF.0)<=2))
DF.0=DF.0[,-Miseria]
taxa=taxa[-Miseria]
OTUs=OTUs[-Miseria]

hit=function(x){min(c(x,1))}
DF.0.hits=as.matrix(DF.0)
DF.0.hits[]=vapply(DF.0.hits, hit, numeric(1))

Unics=data.frame(
Sample=rep(NA,length(which(colSums(DF.0.hits)==1))), OTUs=names(colSums(DF.0)[which(colSums(DF.0.hits)==1)]), Reads=colSums(DF.0)[which(colSums(DF.0.hits)==1)],
            Proportions=rep(0,length(which(colSums(DF.0.hits)==1)))  
)
for (i in 1:length(Unics$OTUs)){
ii=which(DF.0.hits[,Unics$OTUs[i]]==1)  
Unics$Proportions[i]=DF.0[ii,Unics$OTUs[i]]/sum(DF.0[ii,])
Unics$Sample[i]=Samples[ii]}
Unics.Freqs=Unics[Unics$Proportions>=0.05/100,]
row.names(Unics.Freqs)=NULL


DF.0=DF.0[,-which(colSums(DF.0.hits)==1)]
taxa=taxa[-which(colSums(DF.0.hits)==1)]
OTUs=OTUs[-which(colSums(DF.0.hits)==1)]

row.names(DF.0)=Samples[c(1:3,13:15)]

DF=zCompositions::cmultRepl(DF.0,method="GBM",output="p-counts",suppress.print=TRUE,z.warning=0.99)
row.names(DF)=Samples[c(1:3,13:15)]


Type=as.factor(c(rep("CAU_T0", 3),rep("CYM_T0", 3)))
colors=c("green","blue")[Type]

After removing OTUs with 2 or fewer reads across the T0 samples and those appearing in only one of these samples, 1472 taxa remain.

The OTUs removed at this step that represent more than 0.05% of the sample in which they appear are:

Unics.Freqs[rev(order(Unics.Freqs$Proportions)),] %>%
  kbl() %>%
  kable_styling()

Sample	OTUs	Reads	Proportions
CAU_T0_2	OTU966	55	0.0012208

rm(tax_otu)
rm(DF.0.hits)
rm(Miseria)
rm(Unics.Freqs)

6.3.1 How different are the samples?

HC=ClusterHC(DF,Grups=Type,barplot=FALSE,colores=colors)

separacio.global=Sep(HC)

The two sample types are perfectly separated from the start. The separation between groups is 2.43.

We examine the proportion of OTU subsets of reasonable size that already classify them correctly.

> initial_seed=as.integer(Sys.time())
> print (initial_seed)
# [1] 1717567904
initial_seed %% 10000
# [1] 7904

set.seed(7904)
Experimento=function(i)
{
  ii=sample(dim(DF)[2],i,rep=FALSE)
  DFtemp=DF[,ii]
  CC=ClusterHC(DFtemp,dendrograma=FALSE,barplot=FALSE, Grups=Type,colores=colors)
  c(Encerts(CC$tabla,table(Type)),Sep(CC))
}
n=250
F.SS=c()
for (i in 10:750)
  {
  print(i)
  EE=replicate(n,Experimento(i))
  EE.2=EE[2,which(EE[1,]==0)]
XX=replicate(1000,mean(sample(EE.2,n,replace=TRUE)))
  F.SS=rbind(F.SS, c(i,
                     length(EE.2)/250,
                      mean(EE.2),
                      quantile(XX,0.025),
                      quantile(XX,0.975)
  ))
  }
colnames(F.SS)=c("n","proporción","sep. media","Q_0.025","Q_0.975")
saveRDS(F.SS, file="Fraccio.Separadors.T0.RData")

F.SS=readRDS("Fraccio.Separadors.T0.RData")

The first plot shows, for each \(n\) up to half the total number of OTUs, the proportion of samples of size \(n\) that perfectly classify CAU_T0 and CYM_T0 (black curve), along with the 95% Clopper–Pearson confidence interval for that proportion (red curves). We used smoothing splines to smooth the curves.

F.SS_prop.Q_0.025=epitools::binom.exact(F.SS[,2]*250,250)$lower
F.SS_prop.Q_0.975=epitools::binom.exact(F.SS[,2]*250,250)$upper
fit = smooth.spline(F.SS[,1],F.SS[,2],cv=TRUE)
fit.low = smooth.spline(F.SS[,1],F.SS_prop.Q_0.025,cv=TRUE)
fit.up = smooth.spline(F.SS[,1],F.SS_prop.Q_0.975,cv=TRUE)


plot(F.SS[,1:2],pch=20,cex=0.25,col="darkgrey",xlab="n",ylab="Proportion",main="Proportion of perfect classifiers",xlim=c(0,750),xaxp=c(0,750,15),yaxp=c(0,1,10))
lines(fit,col="black",lwd=1)
lines(fit.low,col="red",lwd=1)
lines(fit.up,col="red",lwd=1)

The second plot shows, for each \(n\) up to half the total number of OTUs, the estimated mean separation obtained with a sample of size \(n\) that perfectly classifies CAU_T0 and CYM_T0 (black curve), along with the 95% confidence interval of this mean separation obtained via bootstrap (red curve).

fit = smooth.spline(F.SS[,1],F.SS[,3],cv=TRUE)
fit.low = smooth.spline(F.SS[,1],F.SS[,4],cv=TRUE)
fit.up = smooth.spline(F.SS[,1],F.SS[,5],cv=TRUE)

plot(F.SS[,c(1,3)],pch=20,cex=0.25,col="darkgrey",xlab="n",ylab="Separation",main="Average separation for perfect classifiers",xlim=c(0,750),xaxp=c(0,750,15),yaxp=c(0,2.5,10))
lines(fit,col="black",lwd=1)
lines(fit.low,col="red",lwd=1)
lines(fit.up,col="red",lwd=1)
abline(h=separacio.global,col="green")

`

6.3.2 OTUs significant according to ALDeX

> initial_seed=as.integer(Sys.time())
> print (initial_seed)
# [1] 1717574148
initial_seed %% 10000
# [1] 4148

set.seed(4148)
repl.kw.Cescv2.T0=aldexCesc.clr(t(DF), conds=Type, mc.samples=1000, verbose=FALSE)
aldex.kw.Cescv2.T0=aldex.kw(repl.kw.Cescv2.T0, verbose=FALSE)
#'
saveRDS(aldex.kw.Cescv2.T0, file="aldex_kw_Cescv2.T0.RData")

Taxa with statistically significant differences:

p.valores_kw=readRDS("aldex_kw_Cescv2.T0.RData") 

length(p.valores_kw[p.valores_kw[,2]<0.05,2]) #K-W adjusted p-value < 0.05

## [1] 0

length(p.valores_kw[p.valores_kw[,1]<0.05,2]) #p-value < 0.05

## [1] 121

length(p.valores_kw[p.valores_kw[,1]<0.01,4]) #p-value < 0.01

## [1] 0

There is no OTU with an adjusted Kruskal–Wallis test p-value < 0.05. There are 121 with an unadjusted p-value < 0.05 (and none < 0.01). They classify the samples correctly:

sep.kw.005=QQ.HC.noadjust(p.valores_kw,DF,Type,q=0.05,1,BP=FALSE)

kw.005=which(p.valores_kw[,2]<0.001) 

The separation between groups is 3.43.

Significant=data.frame(
  OTUs=paste("OTU",1:n.OTUs.original,sep=""),
  taxa=taxa.original,
  Aldex.kw.0.05=Indicador(kw.005)
)

6.3.3 Taxa with maximum relevant log-ratios

LRS=explore_logratios(DF,Type)
saveRDS(LRS, file="LRS_T0.RData")

LRS=readRDS("LRS_T0.RData")

assoc=rep(0,dim(DF)[2]-4)
for (m in 5:dim(DF)[2]){
    assoc[m-4]=sum(LRS$`association log-ratio with y`[1:m,1:m])/m^2
}
saveRDS(assoc, file="assoc_T0.RData")

assoc=readRDS("assoc_T0.RData")
plot(5:200,assoc[1:196],type="b",xlab="m",ylab="Bondad mediana de los m más relevantes"
     ,pch=20,cex=0.5)

m=4+which.max(assoc)
impLR=sort(as.numeric(LRS$`order of importance`[1:m]))
DF.Imp=DF[,impLR]
HC=ClusterHC(DF.Imp,dendrograma=FALSE,barplot=FALSE, Grups=Type)
LR.max=c(length(impLR),Sep(HC))

The maximum is attained at the set of 549 most logratio-relevant taxa.
They perfectly separate the two sample types. The separation between groups is 2.83.

Note In the plot we can observe a very pronounced local maximum at 46. Let us examine it:

m0=4+which.max(assoc[1:100])
impLR.2=sort(as.numeric(LRS$`order of importance`[1:m0]))
DF.Imp.0=DF[,impLR.2]
HC=ClusterHC(DF.Imp.0,dendrograma=TRUE,barplot=FALSE, Grups=Type)

LR.max.2=c(length(impLR.2),Sep(HC))

They also perfectly separate the two sample types. The separation between groups is 4.66. Fewer taxa, but better separation.

Significant=cbind(Significant,
                     Log_ratio.max=Indicador(impLR),
                     Log_ratio.max2=Indicador(impLR.2))

6.3.4 Taxa relevant for the bacterial signature (according to coda_glmnet)

coda.glmnet=coda_glmnet(DF,Type,showPlots = FALSE)
saveRDS(coda.glmnet, file="coda.glmnet.T0.RData")

coda.glmnet=readRDS("coda.glmnet.T0.RData")
coda.glmnet$`signature plot`

impGLMNET=coda.glmnet$taxa.num
DF.Imp=DF[,impGLMNET]
HC=ClusterHC(DF.Imp,dendrograma=TRUE,barplot=FALSE,Grups=Type,colores=colors)

glmnet.no0=c(length(coda.glmnet$taxa.num),Sep(HC))

There are 350 significant taxa.
The separation between groups is 2.78.

Significant=cbind(Significant,
glmnet_sign.no0.CAU=Indicador(coda.glmnet$taxa.num[coda.glmnet$`log-contrast coefficients`>0]),
glmnet_sign.no0.CYM=Indicador(coda.glmnet$taxa.num[coda.glmnet$`log-contrast coefficients`<0]))

Out of curiosity, we use 3 replicates to see what happens.

> initial_seed=as.integer(Sys.time())
> print (initial_seed)
# [1] 1717687628
initial_seed %% 10000
# [1] 7628

M=3
set.seed(7628)
repls=aldexCesc.clr(t(DF), conds=Type, mc.samples=M)@analysisData

## [1] "operating in serial mode"

repls=t(cbind(
  repls$CAU_T0_1,repls$CAU_T0_2,repls$CAU_T0_3,
    repls$CYM_T0_1,repls$CYM_T0_2,repls$CYM_T0_3
  ))
attr(repls,"dimnames")[[2]]=NULL
colnames(repls)=colnames(DF)
row.names(repls)=c(
  paste("CAU_T0_1",1:M,sep="_"),
  paste("CAU_T0_2",1:M,sep="_"),
  paste("CAU_T0_3",1:M,sep="_"),
  paste("CYM_T0_1",1:M,sep="_"),
  paste("CYM_T0_2",1:M,sep="_"),
  paste("CYM_T0_3",1:M,sep="_")
  )
mostres_ext=rbind(repls,easyCODA::CLR(DF)$LR)
conds_ext=as.factor(c(rep("CAU", 3*M),rep("CYM", 3*M),rep("CAU", 3),rep("CYM", 3)))
colors_ext=c("green","blue")[conds_ext]
rm(repls)

LogRat_mostres_ext_T0=logratios_matrix_clr(mostres_ext)
saveRDS(LogRat_mostres_ext_T0, file="LogRat_mostres_ext_T0.RData")

LogRat_mostres_ext_T0=readRDS("LogRat_mostres_ext_T0.RData")
LogRat_mostres_ext_T0=list(LogRat_mostres_ext_T0[[1]],LogRat_mostres_ext_T0[[2]])

coda.glmnet_ext=coda_glmnet_lr_bin(LogRat_mostres_ext_T0,conds_ext,taxa,showPlots = FALSE)

coda.glmnet_ext$`signature plot`

impGLMNET_ext=coda.glmnet_ext$taxa.num
DF.Imp=DF[,impGLMNET_ext]
HC=ClusterHC(DF.Imp,dendrograma=TRUE,barplot=FALSE,Grups=Type,colores=colors)

glmnet.ext=c(length(impGLMNET_ext),Sep(HC))

There are 104 significant taxa.
The separation between groups is 4.42.

Significant=cbind(Significant,
glmnet_sign.ext.CAU=Indicador(coda.glmnet_ext$taxa.num[coda.glmnet_ext$`log-contrast coefficients`>0]),
glmnet_sign.ext.CYM=Indicador(coda.glmnet_ext$taxa.num[coda.glmnet_ext$`log-contrast coefficients`<0]))

6.4 Simper

DF.prop=DF.0.total[c(1:3,13:15),]/rowSums(DF.0.total[c(1:3,13:15),])
SMP.prop=simper(DF.prop,group=Type)

indexos_SMP.07=SMP.prop$CAU_T2C_CAU_T2HW$ord[which(SMP.prop$CAU_T2C_CAU_T2HW$cusum<=0.7)]
indexos_SMP.05=SMP.prop$CAU_T2C_CAU_T2HW$ord[which(SMP.prop$CAU_T2C_CAU_T2HW$cusum<=0.5)]
length(indexos_SMP.07)

## [1] 0

length(indexos_SMP.05)

## [1] 0

We find no significant taxon.

6.4.1 Summary

write.csv2(Significant,"OTU_Significativos_CAUT0vsCYMT0.csv",row.names=FALSE)

Resultados=rbind(
LR.max,
LR.max.2,
sep.kw.005,
glmnet.no0,
glmnet.ext)
row.names(Resultados)=c(
"LR.max",
"LR.max.local",
"Aldex",
"glmnet",
"glmnet.ext"
)
colnames(Resultados)=c("Size","Separation")

fit = smooth.spline(F.SS[,1],F.SS[,3],cv=TRUE)
fit.low = smooth.spline(F.SS[,1],F.SS[,4],cv=TRUE)
fit.up = smooth.spline(F.SS[,1],F.SS[,5],cv=TRUE)

plot(F.SS[,c(1,3)],pch=20,cex=0.25,col="darkgrey",xlab="n",ylab="Separation",main="Average separation for perfect classifiers",xlim=c(0,750),xaxp=c(0,750,15),ylim=c(0,7),yaxp=c(0,7,28))
lines(fit,col="black",lwd=1)
lines(fit.low,col="red",lwd=1)
lines(fit.up,col="red",lwd=1)
abline(h=separacio.global,col="green")

points(Resultados,col="blue",type="h")
points(Resultados,col="blue",pch=20)
text(Resultados[,1],Resultados[,2]+0.1,col="blue",labels=row.names(Resultados),cex=0.75)
text(20,separacio.global+0.01,col="green",labels="Global",cex=0.75)

Finally, we intersect the OTUs identified as significant according to LR and coda_glmnet.

Significant.capat=Significant[,c(1,2,4,6,7)]
Significant.capat=cbind(Significant.capat,Cuánto=rowSums(Significant.capat[,3:dim(Significant.capat)[2]]))
Significant.capat=Significant.capat[Significant.capat$Cuánto==2,]

DF.Imp=DF[,Significant.capat[,1]]
HC=ClusterHC(DF.Imp,dendrograma=TRUE,barplot=FALSE,Grups=Type,colores=colors)

There are 312 taxa. They are:

Significant.capat[,1:2]%>%
  kbl() %>%
  kable_styling() 

	OTUs	taxa
1	OTU1	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Thiotrichales.f__Thiotrichaceae.guncultured.
2	OTU2	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Flavobacteriales.f__Flavobacteriaceae.g__Actibacter.s__uncultured_Bacteroidetes
3	OTU3	d__Bacteria.p__Desulfobacterota.c__Desulfobulbia.o__Desulfobulbales.f__Desulfocapsaceae.g__uncultured.s__uncultured_delta
4	OTU4	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Flavobacteriales.f__Flavobacteriaceae.g__Robiginitalea.s__bacterium_AMSU
7	OTU7	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria....
8	OTU8	d__Bacteria.p__Chloroflexi.c__Anaerolineae.o__Anaerolineales.f__Anaerolineaceae.g__uncultured.s__uncultured_organism
9	OTU9	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfobacterales.f__Desulfosarcinaceae.gSva0081_sediment_group.
10	OTU10	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Cytophagales.f__Cyclobacteriaceae.guncultured.
12	OTU12	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Bacteroidales.f__Bacteroidetes_BD2.2.gBacteroidetes_BD2.2.
13	OTU13	d__Bacteria.p__Desulfobacterota.c__Desulfobulbia.o__Desulfobulbales.f__Desulfocapsaceae.guncultured.
15	OTU15	d__Bacteria.p__Firmicutes.c__Clostridia.o__Clostridia.f__Hungateiclostridiaceae.g__uncultured.s__uncultured_bacterium
16	OTU16	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfobacterales.f__Desulfosarcinaceae..
18	OTU18	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Thiotrichales.f__Thiotrichaceae.g__uncultured.s__uncultured_sediment
19	OTU19	d__Bacteria.p__Chloroflexi.c__Anaerolineae.o__Anaerolineales.f__Anaerolineaceae.guncultured.
20	OTU20	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Flavobacteriales.f__Flavobacteriaceae.g__Robiginitalea.s__uncultured_bacterium
22	OTU22	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfobacterales.f__Desulfosarcinaceae.g__Desulfatitalea.s__uncultured_Desulfobacteraceae
23	OTU23	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Sphingobacteriales.f__Lentimicrobiaceae.gLentimicrobiaceae.
24	OTU24	d__Bacteria.p__Bacteroidota.c__Bacteroidia.oBacteroidales...
25	OTU25	d__Archaea.p__Asgardarchaeota.c__Heimdallarchaeia.o__Heimdallarchaeia.f__Heimdallarchaeia.g__Heimdallarchaeia.s__uncultured_archaeon
26	OTU26	d__Bacteria.p__Chloroflexi.c__Anaerolineae.o__SBR1031.f__SBR1031.g__SBR1031.s__uncultured_organism
28	OTU28	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Chromatiales.f__Chromatiaceae.g__Candidatus_Thiobios.s__uncultured_sediment
29	OTU29	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Milano.WF1B.44.f__Milano.WF1B.44.g__Milano.WF1B.44.s__uncultured_gamma
30	OTU30	d__Bacteria.p__Bacteroidota.c__Ignavibacteria.o__Ignavibacteriales.f__PHOS.HE36.g__PHOS.HE36.s__uncultured_bacterium
31	OTU31	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.oEctothiorhodospirales...
32	OTU32	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfobacterales.f__Desulfosarcinaceae.guncultured.
33	OTU33	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Bacteroidetes_VC2.1_Bac22.f__Bacteroidetes_VC2.1_Bac22.g__Bacteroidetes_VC2.1_Bac22.s__uncultured_Bacteroidetes
35	OTU35	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfobacterales.f__Desulfosarcinaceae.g__LCP.80.s__uncultured_delta
36	OTU36	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Steroidobacterales.f__Woeseiaceae.gWoeseia.
37	OTU37	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__KI89A_clade.f__KI89A_clade.gKI89A_clade.
38	OTU38	Unassigned.__.....__
39	OTU39	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Sphingobacteriales.f__Lentimicrobiaceae.g__Lentimicrobiaceae.s__uncultured_Bacteroidetes
40	OTU40	d__Bacteria.p__Chloroflexi.c__Anaerolineae.o__Anaerolineales.f__Anaerolineaceae.g__Pelolinea.s__uncultured_bacterium
41	OTU41	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__B2M28.f__B2M28.gB2M28.
42	OTU42	d__Bacteria.p__Myxococcota.c__Polyangia.o__Polyangiales.f__Sandaracinaceae.guncultured.
43	OTU43	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__uncultured.f__uncultured.g__uncultured.s__uncultured_Thioalkalivibrio
44	OTU44	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfobacterales.f__Desulfosarcinaceae.gSEEP.SRB1.
45	OTU45	d__Bacteria.p__Desulfobacterota.c__Desulfobulbia.o__Desulfobulbales.f__Desulfocapsaceae..
47	OTU47	d__Archaea.p__Nanoarchaeota.c__Nanoarchaeia.o__Woesearchaeales.f__SCGC_AAA011.D5.g__SCGC_AAA011.D5.s__uncultured_euryarchaeote
49	OTU49	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Chromatiales.f__Sedimenticolaceae.g__Candidatus_Thiodiazotropha.s__Candidatus_Thiodiazotropha
50	OTU50	d__Bacteria.p__Sva0485.c__Sva0485.o__Sva0485.f__Sva0485.gSva0485.
52	OTU52	d__Bacteria.p__Actinobacteriota.c__Acidimicrobiia.o__Actinomarinales.f__uncultured.guncultured.
53	OTU53	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__uncultured.f__uncultured.guncultured.
54	OTU54	d__Bacteria.p__Actinobacteriota.c__Acidimicrobiia.o__Microtrichales.f__Ilumatobacteraceae.gIlumatobacter.
55	OTU55	d__Bacteria.p__Calditrichota.c__Calditrichia.o__Calditrichales.f__Calditrichaceae.g__Caldithrix.s__uncultured_bacterium
56	OTU56	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Arenicellales.f__Arenicellaceae.guncultured.
57	OTU57	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Flavobacteriales.f__Flavobacteriaceae.gEudoraea.
60	OTU60	d__Bacteria.p__Calditrichota.c__Calditrichia.o__Calditrichales.f__Calditrichaceae.g__Calditrichaceae.s__uncultured_bacterium
62	OTU62	d__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Rhodobacterales.f__Rhodobacteraceae..
64	OTU64	d__Eukaryota......
69	OTU69	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Chromatiales.f__Sedimenticolaceae..
70	OTU70	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.oDesulfobacterales...
71	OTU71	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Flavobacteriales.f__Flavobacteriaceae.gRobiginitalea.
72	OTU72	d__Bacteria.p__Calditrichota.c__Calditrichia.o__Calditrichales.f__Calditrichaceae.g__Calorithrix.s__uncultured_bacterium
73	OTU73	d__Bacteria.p__Bacteroidota.c__Kryptonia.o__Kryptoniales.f__BSV26.gBSV26.
77	OTU77	d__Archaea.p__Thermoplasmatota.c__Thermoplasmata.o__uncultured.f__uncultured.g__uncultured.s__uncultured_Thermoplasmatales
79	OTU79	d__Bacteria.p__Acidobacteriota.c__Subgroup_21.o__Subgroup_21.f__Subgroup_21.g__Subgroup_21.s__uncultured_bacterium
80	OTU80	d__Bacteria......
81	OTU81	d__Bacteria.p__Latescibacterota.c__Latescibacterota.o__Latescibacterota.f__Latescibacterota.g__Latescibacterota.s__uncultured_bacterium
82	OTU82	d__Bacteria.p__Calditrichota.c__Calditrichia.o__Calditrichales.f__Calditrichaceae.g__Caldithrix.s__uncultured_delta
83	OTU83	d__Bacteria.p__SAR324_clade.Marine_group_B..c__SAR324_clade.Marine_group_B..o__SAR324_clade.Marine_group_B..f__SAR324_clade.Marine_group_B..gSAR324_clade.Marine_group_B..
84	OTU84	d__Bacteria.p__Latescibacterota.c__Latescibacteria.o__Latescibacterales.f__Latescibacteraceae.g__Latescibacteraceae.s__uncultured_bacterium
85	OTU85	d__Bacteria.pChloroflexi.....
88	OTU88	d__Bacteria.p__Spirochaetota.c__Spirochaetia.o__Spirochaetales.f__Spirochaetaceae.gSpirochaeta_2.
94	OTU94	d__Bacteria.p__Spirochaetota.c__Spirochaetia.o__Spirochaetales.f__Spirochaetaceae.g__Spirochaeta.s__uncultured_bacterium
95	OTU95	d__Bacteria.p__Cloacimonadota.c__Cloacimonadia.o__Cloacimonadales.f__MSBL8.g__MSBL8.s__uncultured_bacterium
98	OTU98	d__Bacteria.p__Acetothermia.c__Acetothermiia.o__Acetothermiia.f__Acetothermiia.gAcetothermiia.
102	OTU102	d__Bacteria.p__Bacteroidota.c__Ignavibacteria.o__Ignavibacteriales.f__Melioribacteraceae.g__IheB3.7.s__uncultured_Chlorobi
104	OTU104	d__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Rhizobiales.f__Hyphomicrobiaceae..
105	OTU105	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Chromatiales.f__Chromatiaceae.gHalochromatium.
108	OTU108	d__Bacteria.p__Spirochaetota.c__Spirochaetia.o__Spirochaetales.f__Spirochaetaceae.gGWE2.31.10.
111	OTU111	d__Bacteria.p__Chloroflexi.c__Anaerolineae.o__Ardenticatenales.f__uncultured.guncultured.
113	OTU113	d__Archaea.p__Altiarchaeota.c__Altiarchaeia.o__Altiarchaeales.f__Altiarchaeaceae.g__Candidatus_Altiarchaeum.s__uncultured_archaeon
116	OTU116	d__Bacteria.p__Zixibacteria.c__Zixibacteria.o__Zixibacteria.f__Zixibacteria.g__Zixibacteria.s__uncultured_bacterium
118	OTU118	d__Archaea.p__Thermoplasmatota.c__Thermoplasmata.o__Marine_Benthic_Group_D_and_DHVEG.1.f__Marine_Benthic_Group_D_and_DHVEG.1.g__Marine_Benthic_Group_D_and_DHVEG.1.s__uncultured_archaeon
119	OTU119	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Bacteroidales.f__Marinilabiliaceae.g__uncultured.s__uncultured_Bacteroidetes
120	OTU120	d__Bacteria.p__Desulfobacterota.c__Desulfobulbia.o__Desulfobulbales.f__Desulfobulbaceae.gDesulfobulbus.
122	OTU122	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Bacteroidales.f__Marinilabiliaceae.guncultured.
123	OTU123	d__Bacteria.p__Planctomycetota.c__Planctomycetes.o__Pirellulales.f__Pirellulaceae.gPir4_lineage.
124	OTU124	d__Bacteria.p__Spirochaetota.c__Spirochaetia.o__Spirochaetales.f__Spirochaetaceae.g__GWE2.31.10.s__uncultured_gamma
130	OTU130	d__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__SAR11_clade.f__Clade_III.gClade_III.
132	OTU132	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__BD7.8.f__BD7.8.gBD7.8.
133	OTU133	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfatiglandales.f__Desulfatiglandaceae.gDesulfatiglans.
135	OTU135	d__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__SAR11_clade.f__Clade_I.gClade_Ia.
136	OTU136	d__Bacteria.p__Patescibacteria.c__Parcubacteria.o__Candidatus_Kaiserbacteria.f__Candidatus_Kaiserbacteria.g__Candidatus_Kaiserbacteria.s__uncultured_bacterium
139	OTU139	d__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Micavibrionales.f__Micavibrionaceae.g__uncultured.s__uncultured_bacterium
140	OTU140	d__Bacteria.p__Cyanobacteria.c__Cyanobacteriia.o__Cyanobacteriales.f__Cyanobacteriaceae..
144	OTU144	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Flavobacteriales.f__Flavobacteriaceae.gAquibacter.
146	OTU146	d__Bacteria.p__Spirochaetota.c__Spirochaetia.o__Spirochaetales.f__Spirochaetaceae.g__GWE2.31.10.s__uncultured_bacterium
147	OTU147	d__Bacteria.p__Nitrospirota.c__Thermodesulfovibrionia.o__uncultured.f__uncultured.g__uncultured.s__uncultured_Nitrospirae
148	OTU148	d__Bacteria.p__Verrucomicrobiota.c__Kiritimatiellae.o__Kiritimatiellales.f__Kiritimatiellaceae.gR76.B128.
149	OTU149	d__Bacteria.p__Acidobacteriota.c__Subgroup_18.o__Subgroup_18.f__Subgroup_18.gSubgroup_18.
150	OTU150	d__Archaea......
152	OTU152	d__Bacteria.p__Verrucomicrobiota.c__Verrucomicrobiae.o__Pedosphaerales.f__Pedosphaeraceae.g__DEV008.s__uncultured_bacterium
153	OTU153	d__Archaea.p__Thermoplasmatota.c__Thermoplasmata.o__uncultured.f__uncultured.g__uncultured.s__uncultured_archaeon
155	OTU155	d__Bacteria.p__Bacteroidota.c__Ignavibacteria.o__Ignavibacteriales.f__Melioribacteraceae.g__IheB3.7.s__uncultured_sediment
156	OTU156	d__Bacteria.p__Spirochaetota.c__Spirochaetia.o__Spirochaetales.f__Spirochaetaceae.g__Spirochaeta_2.s__uncultured_bacterium
157	OTU157	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfobacterales.f__Desulfosarcinaceae.g__SEEP.SRB1.s__Olavius_ilvae
158	OTU158	d__Bacteria.p__Spirochaetota.c__Spirochaetia.o__Spirochaetales.f__Spirochaetaceae.g__Sediminispirochaeta.s__uncultured_bacterium
159	OTU159	d__Bacteria.pAcidobacteriota.....
160	OTU160	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Chitinophagales.f__Saprospiraceae.g__uncultured.s__uncultured_Alphaproteobacteria
161	OTU161	d__Bacteria.p__Chloroflexi.c__Anaerolineae.o__Caldilineales.f__Caldilineaceae.guncultured.
162	OTU162	d__Bacteria.p__Gemmatimonadota.c__PAUC43f_marine_benthic_group.o__PAUC43f_marine_benthic_group.f__PAUC43f_marine_benthic_group.g__PAUC43f_marine_benthic_group.s__uncultured_actinobacterium
168	OTU168	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Thiomicrospirales.f__Thiomicrospiraceae.gendosymbionts.
169	OTU169	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Gammaproteobacteria_Incertae_Sedis.f__Unknown_Family.guncultured.
173	OTU173	d__Bacteria.p__Calditrichota.c__Calditrichia.o__Calditrichales.f__Calditrichaceae.g__Caldithrix.s__uncultured_Deferribacteres
175	OTU175	d__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Caulobacterales.f__Hyphomonadaceae..
181	OTU181	d__Bacteria.p__Chloroflexi.c__Anaerolineae....
185	OTU185	d__Bacteria.p__Patescibacteria.c__WWE3.o__WWE3.f__WWE3.g__WWE3.s__uncultured_bacterium
189	OTU189	d__Bacteria.p__Firmicutes.c__Clostridia.o__Lachnospirales.f__Defluviitaleaceae.g__Defluviitaleaceae_UCG.011.s__uncultured_bacterium
190	OTU190	d__Bacteria.p__Myxococcota.c__Polyangia.o__Polyangiales.f__Sandaracinaceae.g__uncultured.s__bacterium_enrichment
191	OTU191	d__Archaea.p__Nanoarchaeota.c__Nanoarchaeia.o__Woesearchaeales.f__Woesearchaeales.g__Woesearchaeales.s__uncultured_crenarchaeote
192	OTU192	d__Bacteria.p__Planctomycetota.c__Planctomycetes.o__Pirellulales.f__Pirellulaceae.gRhodopirellula.
194	OTU194	d__Bacteria.p__Spirochaetota.c__Spirochaetia.o__Spirochaetales.f__Spirochaetaceae.g__Spirochaeta_2.s__Spirochaeta_isovalerica
204	OTU204	d__Bacteria.p__Chloroflexi.c__Anaerolineae.o__SBR1031.f__SBR1031.g__SBR1031.s__metagenome
205	OTU205	d__Bacteria.p__Spirochaetota.c__Spirochaetia.o__Spirochaetales.f__Spirochaetaceae.gSediminispirochaeta.
208	OTU208	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Flavobacteriales.f__Flavobacteriaceae.gLutibacter.
211	OTU211	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfobacterales.f__Desulfosarcinaceae.g__Desulfosarcina.s__uncultured_marine
213	OTU213	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfobacterales.f__Desulfosarcinaceae.gDesulfatitalea.
216	OTU216	d__Bacteria.p__Actinobacteriota.c__WCHB1.81.o__WCHB1.81.f__WCHB1.81.g__WCHB1.81.s__uncultured_bacterium
217	OTU217	d__Bacteria.p__Desulfobacterota.c__Desulfobulbia.o__Desulfobulbales.f__Desulfobulbaceae.g__Desulfobulbus.s__uncultured_bacterium
222	OTU222	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Bacteroidales.f__Prolixibacteraceae.gSunxiuqinia.
226	OTU226	d__Bacteria.p__Chloroflexi.c__Anaerolineae.o__KZNMV.5.B42.f__KZNMV.5.B42.gKZNMV.5.B42.
228	OTU228	d__Bacteria.p__Verrucomicrobiota.c__Lentisphaeria.o__Oligosphaerales.f__Lenti.02.g__Lenti.02.s__uncultured_bacterium
230	OTU230	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Cytophagales.f__Cyclobacteriaceae.g__uncultured.s__uncultured_Bacteroidetes
231	OTU231	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Chromatiales.f__Chromatiaceae..
232	OTU232	d__Bacteria.p__Chloroflexi.c__KD4.96.o__KD4.96.f__KD4.96.gKD4.96.
236	OTU236	d__Bacteria.p__Bacteroidota.c__Kryptonia.o__Kryptoniales.f__MSB.3C8.gMSB.3C8.
237	OTU237	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Gammaproteobacteria_Incertae_Sedis.f__Unknown_Family.g__uncultured.s__uncultured_marine
239	OTU239	d__Bacteria.p__Zixibacteria.c__Zixibacteria.o__Zixibacteria.f__Zixibacteria.gZixibacteria.
242	OTU242	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Gammaproteobacteria_Incertae_Sedis.f__Unknown_Family.g__Unknown_Family.s__uncultured_bacterium
249	OTU249	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Chromatiales.f__Sedimenticolaceae.guncultured.
252	OTU252	d__Bacteria.p__Verrucomicrobiota.c__Verrucomicrobiae.o__Verrucomicrobiales.f__DEV007.gDEV007.
253	OTU253	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfatiglandales.f__Desulfatiglandaceae.g__Desulfatiglans.s__uncultured_delta
260	OTU260	d__Bacteria.p__Planctomycetota.c__Phycisphaerae.o__CCM11a.f__CCM11a.g__CCM11a.s__uncultured_organism
266	OTU266	d__Bacteria.p__Patescibacteria.c__ABY1.o__Candidatus_Kerfeldbacteria.f__Candidatus_Kerfeldbacteria.g__Candidatus_Kerfeldbacteria.s__uncultured_bacterium
267	OTU267	d__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Caulobacterales.f__Hyphomonadaceae.guncultured.
274	OTU274	d__Bacteria.p__Chloroflexi.c__Anaerolineae.o__Anaerolineales.f__Anaerolineaceae.g__Thermomarinilinea.s__uncultured_bacterium
276	OTU276	d__Bacteria.p__Proteobacteria.c__Alphaproteobacteria....
277	OTU277	d__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Kiloniellales.f__Kiloniellaceae.gTistlia.
284	OTU284	d__Bacteria.p__LCP.89.c__LCP.89.o__LCP.89.f__LCP.89.g__LCP.89.s__saltmarsh_clone
292	OTU292	d__Archaea.p__Thermoplasmatota.c__Thermoplasmatota.o__Thermoplasmatota.f__Thermoplasmatota.g__uncultured.s__uncultured_archaeon
293	OTU293	d__Archaea.p__Aenigmarchaeota.c__Deep_Sea_Euryarchaeotic_Group.DSEG..o__Deep_Sea_Euryarchaeotic_Group.DSEG..f__Deep_Sea_Euryarchaeotic_Group.DSEG..g__Deep_Sea_Euryarchaeotic_Group.DSEG..s__uncultured_archaeon
300	OTU300	d__Bacteria.p__Spirochaetota.c__Spirochaetia.o__Spirochaetales.f__Spirochaetaceae.g__Sediminispirochaeta.s__uncultured_Spirochaetes
304	OTU304	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Flavobacteriales.f__Flavobacteriaceae.gMaritimimonas.
305	OTU305	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Chitinophagales.f__Saprospiraceae.g__uncultured.s__uncultured_organism
307	OTU307	d__Archaea.p__Nanoarchaeota.c__Nanoarchaeia.oWoesearchaeales...
314	OTU314	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__UBA10353_marine_group.f__UBA10353_marine_group.g__UBA10353_marine_group.s__uncultured_bacterium
318	OTU318	d__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Rhizobiales.f__Hyphomicrobiaceae.g__Filomicrobium.s__uncultured_Alphaproteobacteria
328	OTU328	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfobacterales.f__Desulfosarcinaceae.g__Desulfatirhabdium.s__uncultured_delta
334	OTU334	d__Bacteria.p__Planctomycetota.c__Phycisphaerae.o__MSBL9.f__SG8.4.gSG8.4.
337	OTU337	d__Bacteria.p__Chloroflexi.c__Anaerolineae.o__SJA.15.f__SJA.15.g__SJA.15.s__uncultured_Chloroflexi
340	OTU340	d__Bacteria.p__Patescibacteria.c__Gracilibacteria.o__Absconditabacteriales_.SR1..f_Absconditabacteriales.SR1..g_Absconditabacteriales.SR1..s__uncultured_bacterium
341	OTU341	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Flavobacteriales.f__Crocinitomicaceae.g__Crocinitomix.s__uncultured_bacterium
353	OTU353	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Oceanospirillales.f__Nitrincolaceae.guncultured.
354	OTU354	d__Bacteria.p__Spirochaetota.c__Spirochaetia.o__Spirochaetales.f__Spirochaetaceae.g__Spirochaeta_2.s__uncultured_Spirochaetes
356	OTU356	d__Bacteria.p__Planctomycetota.c__Phycisphaerae.o__CCM11a.f__CCM11a.g__CCM11a.s__uncultured_bacterium
358	OTU358	d__Bacteria.p__Elusimicrobiota.c__Lineage_IIb.o__Lineage_IIb.f__Lineage_IIb.g__Lineage_IIb.s__uncultured_bacterium
368	OTU368	d__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Rhodobacterales.f__Rhodobacteraceae.gHIMB11.
371	OTU371	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Flavobacteriales.f__Flavobacteriaceae.g__Maritimimonas.s__uncultured_organism
372	OTU372	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Oceanospirillales.f__Pseudohongiellaceae.gPseudohongiella.
381	OTU381	d__Bacteria.p__Patescibacteria.c__Gracilibacteria.o__Candidatus_Peregrinibacteria.f__Candidatus_Peregrinibacteria.g__Candidatus_Peregrinibacteria.s__uncultured_bacterium
386	OTU386	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Vibrionales.f__Vibrionaceae.gVibrio.
389	OTU389	d__Bacteria.p__Bdellovibrionota.c__Bdellovibrionia.o__Bacteriovoracales.f__Bacteriovoracaceae.g__Peredibacter.s__uncultured_bacterium
390	OTU390	d__Bacteria.p__Latescibacterota.c__Latescibacterota.o__Latescibacterota.f__Latescibacterota.g__Latescibacterota.s__uncultured_organism
392	OTU392	d__Archaea.p__Asgardarchaeota.c__Odinarchaeia.o__Odinarchaeia.f__Odinarchaeia.g__Odinarchaeia.s__uncultured_marine
393	OTU393	d__Bacteria.p__Latescibacterota.c__Latescibacteria.o__Latescibacterales.f__Latescibacteraceae.g__Latescibacteraceae.s__uncultured_actinobacterium
394	OTU394	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfobacterales.f__Desulfosarcinaceae.g__Sva0081_sediment_group.s__uncultured_marine
397	OTU397	d__Bacteria.p__NB1.j.c__NB1.j.o__NB1.j.f__NB1.j.gNB1.j.
400	OTU400	d__Bacteria.p__Planctomycetota.c__Phycisphaerae.o__CCM11a.f__CCM11a.gCCM11a.
401	OTU401	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Bacteroidales.f__Marinilabiliaceae.g__Labilibacter.s__uncultured_Bacteroidetes
402	OTU402	d__Bacteria.p__Acetothermia.c__Acetothermiia.o__Acetothermiia.f__Acetothermiia.g__Acetothermiia.s__uncultured_organism
421	OTU421	d__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Micavibrionales.f__uncultured.guncultured.
424	OTU424	d__Bacteria.p__Gemmatimonadota.c__PAUC43f_marine_benthic_group.o__PAUC43f_marine_benthic_group.f__PAUC43f_marine_benthic_group.gPAUC43f_marine_benthic_group.
426	OTU426	d__Bacteria.p__Verrucomicrobiota.c__Omnitrophia.o__Omnitrophales.f__Omnitrophaceae.g__Candidatus_Omnitrophus.s__uncultured_bacterium
435	OTU435	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfobacterales.f__Desulfobacteraceae.gDesulfobacter.
436	OTU436	d__Bacteria.p__Desulfobacterota.c__Desulfuromonadia.o__Bradymonadales.f__Bradymonadales.gBradymonadales.
448	OTU448	d__Bacteria.p__Patescibacteria.c__ABY1.o__Candidatus_Falkowbacteria.f__Candidatus_Falkowbacteria.gCandidatus_Falkowbacteria.
453	OTU453	d__Bacteria.p__Modulibacteria.c__Moduliflexia.o__Moduliflexales.f__Moduliflexaceae.gModuliflexaceae.
463	OTU463	d__Bacteria.p__Chloroflexi.c__Anaerolineae.o__RBG.13.54.9.f__RBG.13.54.9.g__RBG.13.54.9.s__uncultured_bacterium
475	OTU475	d__Bacteria.p__Chloroflexi.c__Dehalococcoidia.o__GIF9.f__AB.539.J10.g__SCGC.AB.539.J10.s__uncultured_bacterium
476	OTU476	d__Bacteria.p__Myxococcota.c__Polyangia.o__MidBa8.f__MidBa8.g__MidBa8.s__uncultured_delta
480	OTU480	d__Bacteria.p__Calditrichota.c__Calditrichia.o__Calditrichales.f__Calditrichaceae.g__Calditrichaceae.s__uncultured_organism
482	OTU482	d__Bacteria.p__Cyanobacteria.c__Cyanobacteriia.o__Chloroplast.f__Chloroplast.g__Chloroplast.s__Chromerida_sp.
483	OTU483	d__Bacteria.p__Bdellovibrionota.c__Oligoflexia.o__Oligoflexales.f__uncultured.g__uncultured.s__uncultured_organism
490	OTU490	d__Bacteria.p__Bdellovibrionota.c__Bdellovibrionia.o__Bacteriovoracales.f__Bacteriovoracaceae.gPeredibacter.
495	OTU495	d__Archaea.p__Micrarchaeota.c__Micrarchaeia.o__Micrarchaeales.f__Micrarchaeales.g__Micrarchaeales.s__uncultured_euryarchaeote
501	OTU501	d__Bacteria.p__Latescibacterota.c__Latescibacterota.o__Latescibacterota.f__Latescibacterota.g__Latescibacterota.s__uncultured_Bacteroidetes
503	OTU503	d__Bacteria.p__Fibrobacterota.c__Chitinivibrionia.o__Chitinivibrionales.f__Chitinivibrionaceae.g__possible_genus_03.s__uncultured_bacterium
508	OTU508	d__Bacteria.p__Verrucomicrobiota.c__Verrucomicrobiae.o__Verrucomicrobiales.f__DEV007.g__DEV007.s__uncultured_organism
509	OTU509	d__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Rhodospirillales.f__Rhodospirillaceae.g__Candidatus_Riegeria.s__uncultured_bacterium
530	OTU530	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Thiomicrospirales.f__Thioglobaceae.gSUP05_cluster.
532	OTU532	d__Bacteria.p__Acetothermia.c__Acetothermiia.o__Acetothermiia.f__Acetothermiia.g__Acetothermiia.s__bacterium_enrichment
537	OTU537	d__Bacteria.p__Fermentibacterota.c__Fermentibacteria.o__Fermentibacterales.f__Fermentibacteraceae.g__Fermentibacteraceae.s__uncultured_sediment
539	OTU539	d__Bacteria.p__Patescibacteria.c__Parcubacteria.o__Candidatus_Kaiserbacteria.f__Candidatus_Kaiserbacteria.gCandidatus_Kaiserbacteria.
541	OTU541	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Ga0077536.f__Ga0077536.g__Ga0077536.s__uncultured_gamma
547	OTU547	d__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Rhizobiales.f__Rhizobiales_Incertae_Sedis.gAnderseniella.
553	OTU553	d__Bacteria.p__Campilobacterota.c__Campylobacteria.o__Campylobacterales.f__Helicobacteraceae..
554	OTU554	d__Bacteria.p__Chloroflexi.c__Dehalococcoidia.o__GIF9.f__AB.539.J10.g__AB.539.J10.s__uncultured_bacterium
565	OTU565	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Chitinophagales.f__Saprospiraceae.g__Portibacter.s__uncultured_Bacteroidetes
568	OTU568	d__Bacteria.p__Margulisbacteria.c__Margulisbacteria.o__Margulisbacteria.f__Margulisbacteria.g__Margulisbacteria.s__uncultured_bacterium
570	OTU570	d__Bacteria.p__Chloroflexi.c__Anaerolineae.o__Thermoflexales.f__Thermoflexaceae.gThermoflexus.
574	OTU574	d__Bacteria.p__Planctomycetota.c__Planctomycetes.o__Pirellulales.f__Pirellulaceae.g__uncultured.s__uncultured_organism
585	OTU585	d__Bacteria.p__Bacteroidota.c__Kryptonia.o__Kryptoniales.f__MSB.3C8.g__MSB.3C8.s__uncultured_bacterium
618	OTU618	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Ectothiorhodospirales.f__Ectothiorhodospiraceae.g__Thiogranum.s__uncultured_gamma
620	OTU620	d__Bacteria.p__Firmicutes.c__Clostridia.o__Lachnospirales.f__Lachnospiraceae.g__uncultured.s__Clostridiales_bacterium
622	OTU622	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Chitinophagales.f__uncultured.g__uncultured.s__uncultured_Bacteroidetes
628	OTU628	d__Bacteria.p__Campilobacterota.c__Campylobacteria.o__Campylobacterales.f__Rs.M59_termite_group.g__Rs.M59_termite_group.s__uncultured_bacterium
631	OTU631	d__Bacteria.p__Campilobacterota.c__Campylobacteria.o__Campylobacterales.f__Campylobacteraceae.g__Campylobacter.s__uncultured_Epsilonproteobacteria
657	OTU657	d__Bacteria.p__Actinobacteriota.c__Coriobacteriia.o__OPB41.f__OPB41.g__OPB41.s__unidentified_marine
663	OTU663	d__Bacteria.p__Acidobacteriota.c__Vicinamibacteria.o__Subgroup_9.f__Subgroup_9.g__Subgroup_9.s__uncultured_bacterium
694	OTU694	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Flavobacteriales.f__Flavobacteriaceae.g__NS5_marine_group.s__uncultured_Flavobacterium
700	OTU700	d__Bacteria.p__SAR324_clade.Marine_group_B..c__SAR324_clade.Marine_group_B..o__SAR324_clade.Marine_group_B..f__SAR324_clade.Marine_group_B..g__SAR324_clade.Marine_group_B..s__uncultured_organism
706	OTU706	d__Bacteria.p__Myxococcota.c__Polyangia.o__UASB.TL25.f__UASB.TL25.gUASB.TL25.
708	OTU708	d__Bacteria.p__Patescibacteria.c__Gracilibacteria.o__Gracilibacteria.f__Gracilibacteria.g__Gracilibacteria.s__uncultured_organism
714	OTU714	d__Bacteria.p__Verrucomicrobiota.c__Omnitrophia.o__Omnitrophales.f__Omnitrophales.g__Omnitrophales.s__uncultured_bacterium
729	OTU729	d__Bacteria.p__Patescibacteria.c__Parcubacteria.o__Candidatus_Kaiserbacteria.f__Candidatus_Kaiserbacteria.g__Candidatus_Kaiserbacteria.s__uncultured_organism
742	OTU742	d__Bacteria.p__Planctomycetota.c__Pla4_lineage.o__Pla4_lineage.f__Pla4_lineage.g__Pla4_lineage.s__uncultured_bacterium
750	OTU750	d__Bacteria.p__Desulfobacterota.c__Syntrophobacteria.o__Syntrophobacterales.f__uncultured.g__uncultured.s__uncultured_delta
761	OTU761	d__Bacteria.p__Actinobacteriota.c__Acidimicrobiia.o__Microtrichales.f__Microtrichaceae.gSva0996_marine_group.
776	OTU776	d__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Rhodospirillales.f__Terasakiellaceae.guncultured.
789	OTU789	d__Bacteria.p__Desulfobacterota.c__Desulfobulbia.o__Desulfobulbales.f__Desulfocapsaceae.g__Desulfopila.s__uncultured_bacterium
794	OTU794	d__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Rhodobacterales.f__Rhodobacteraceae.gMarivita.
803	OTU803	d__Archaea.p__Aenigmarchaeota.c__Aenigmarchaeia.o__Aenigmarchaeales.f__Aenigmarchaeales.gAenigmarchaeales.
814	OTU814	d__Archaea.p__Aenigmarchaeota.c__Aenigmarchaeia.o__Aenigmarchaeales.f__Aenigmarchaeales.g__Aenigmarchaeales.s__uncultured_archaeon
823	OTU823	d__Bacteria.p__WS2.c__WS2.o__WS2.f__WS2.g__WS2.s__uncultured_Firmicutes
837	OTU837	d__Bacteria.p__Latescibacterota.c__Latescibacteria.o__Latescibacterales.f__Latescibacteraceae.g__Latescibacteraceae.s__bacterium_enrichment
840	OTU840	d__Bacteria.p__Chloroflexi.c__Dehalococcoidia.o__SAR202_clade.f__SAR202_clade.gSAR202_clade.
845	OTU845	d__Bacteria.p__Dependentiae.c__Babeliae.o__Babeliales.f__Vermiphilaceae.gVermiphilaceae.
897	OTU897	d__Bacteria.p__Chloroflexi.c__Dehalococcoidia.o__GIF9.f__AB.539.J10.gAB.539.J10.
905	OTU905	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Granulosicoccales.f__Granulosicoccaceae.g__Granulosicoccus.s__uncultured_bacterium
908	OTU908	d__Bacteria.p__Verrucomicrobiota.c__Verrucomicrobiae.oOpitutales...
933	OTU933	d__Bacteria.p__Campilobacterota.c__Campylobacteria.o__Campylobacterales.f__Sulfurimonadaceae.g__Sulfurimonas.s__bacterium_enrichment
937	OTU937	d__Bacteria.p__Acidobacteriota.c__Acidobacteriae....
950	OTU950	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__CH2b56.f__CH2b56.g__CH2b56.s__uncultured_bacterium
954	OTU954	d__Bacteria.p__Planctomycetota.c__vadinHA49.o__vadinHA49.f__vadinHA49.g__vadinHA49.s__uncultured_organism
967	OTU967	d__Bacteria.p__Planctomycetota.c__Pla3_lineage.o__Pla3_lineage.f__Pla3_lineage.g__Pla3_lineage.s__uncultured_planctomycete
983	OTU983	d__Bacteria.p__Desulfobacterota.c__Desulfobulbia.o__Desulfobulbales.f__Desulfobulbaceae.g__uncultured.s__uncultured_gamma
987	OTU987	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfobacterales.f__Desulfobacteraceae.g__uncultured.s__uncultured_organism
988	OTU988	d__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Sphingomonadales.f__Sphingomonadaceae.g__Erythrobacter.s__Erythrobacter_longus
989	OTU989	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Chitinophagales.f__Saprospiraceae.g__Lewinella.s__uncultured_organism
991	OTU991	d__Bacteria.p__Acetothermia.c__Acetothermiia.o__Acetothermiia.f__Acetothermiia.g__Acetothermiia.s__uncultured_bacterium
993	OTU993	d__Bacteria.p__Sumerlaeota.c__Sumerlaeia.o__Sumerlaeales.f__Sumerlaeaceae.g__Sumerlaea.s__uncultured_organism
998	OTU998	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Flavobacteriales.f__Flavobacteriaceae.g__Flavobacteriaceae.s__Aureicoccus_marinus
1000	OTU1000	d__Bacteria.p__Cyanobacteria.c__Cyanobacteriia.o__Synechococcales.f__Cyanobiaceae.gCyanobium_PCC.6307.
1001	OTU1001	d__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Paracaedibacterales.f__Paracaedibacteraceae.g__Candidatus_Captivus.s__uncultured_bacterium
1003	OTU1003	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Sphingobacteriales.f__NS11.12_marine_group.g__NS11.12_marine_group.s__uncultured_marine
1013	OTU1013	d__Archaea.p__Nanoarchaeota.c__Nanoarchaeia.o__Woesearchaeales.f__GW2011_GWC1_47_15.gGW2011_GWC1_47_15.
1014	OTU1014	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.oCellvibrionales...
1041	OTU1041	d__Bacteria.p__Verrucomicrobiota.c__Verrucomicrobiae.o__Verrucomicrobiales.f__Rubritaleaceae.g__uncultured.s__uncultured_bacterium
1050	OTU1050	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Chitinophagales.f__uncultured.g__uncultured.s__uncultured_bacterium
1057	OTU1057	d__Bacteria.p__Dependentiae.c__Babeliae.o__Babeliales.f__Babeliales.g__Babeliales.s__uncultured_organism
1064	OTU1064	d__Bacteria.p__Dependentiae.c__Babeliae.o__Babeliales.f__Vermiphilaceae.g__Vermiphilaceae.s__uncultured_delta
1070	OTU1070	d__Bacteria.p__Cyanobacteria.c__Vampirivibrionia.o__Gastranaerophilales.f__Gastranaerophilales.gGastranaerophilales.
1086	OTU1086	d__Bacteria.p__Planctomycetota.c__Planctomycetes.o__Pirellulales.f__Pirellulaceae.gRubripirellula.
1097	OTU1097	d__Bacteria.p__Latescibacterota.c__Latescibacterota.o__Latescibacterota.f__Latescibacterota.g__Latescibacterota.s__unidentified_bacterium
1100	OTU1100	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Cytophagales.f__Cyclobacteriaceae.g__uncultured.s__uncultured_soil
1108	OTU1108	d__Bacteria.p__NB1.j.c__NB1.j.o__NB1.j.f__NB1.j.g__NB1.j.s__uncultured_prokaryote
1114	OTU1114	d__Bacteria.p__Verrucomicrobiota.c__Lentisphaeria.o__SS1.B.02.17.f__SS1.B.02.17.g__SS1.B.02.17.s__uncultured_Lentisphaerae
1121	OTU1121	d__Bacteria.p__Myxococcota.c__Polyangia.o__Polyangiales.f__Eel.36e1D6.g__Eel.36e1D6.s__uncultured_Polyangiaceae
1127	OTU1127	d__Bacteria.p__Actinobacteriota.c__WCHB1.81.o__WCHB1.81.f__WCHB1.81.g__WCHB1.81.s__uncultured_actinobacterium
1129	OTU1129	d__Archaea.p__Thermoplasmatota.c__Thermoplasmata.o__Marine_Benthic_Group_D_and_DHVEG.1.f__Marine_Benthic_Group_D_and_DHVEG.1.g__Marine_Benthic_Group_D_and_DHVEG.1.s__archaeon_enrichment
1142	OTU1142	d__Bacteria.p__Campilobacterota.c__Campylobacteria.o__Campylobacterales.f__Sulfurimonadaceae..
1150	OTU1150	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Chromatiales.f__Chromatiaceae.g__Candidatus_Thiobios.s__uncultured_gamma
1160	OTU1160	d__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Caulobacterales.f__Parvularculaceae.gParvularcula.
1162	OTU1162	d__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Rhodobacterales.f__Rhodobacteraceae.gRoseobacter.
1173	OTU1173	d__Bacteria.p__Actinobacteriota.c__Acidimicrobiia.o__Actinomarinales.f__uncultured.g__uncultured.s__bacterium_WH6.7
1178	OTU1178	d__Bacteria.p__Firmicutes.c__Bacilli.o__Izemoplasmatales.f__Izemoplasmataceae.g__Izimaplasma.s__Candidatus_Izimaplasma
1189	OTU1189	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfobacterales.f__Desulfobacteraceae.g__Desulfospira.s__uncultured_bacterium
1194	OTU1194	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Oceanospirillales.f__Saccharospirillaceae.gReinekea.
1196	OTU1196	d__Bacteria.p__CK.2C2.2.c__CK.2C2.2.o__CK.2C2.2.f__CK.2C2.2.g__CK.2C2.2.s__uncultured_organism
1198	OTU1198	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Flavobacteriales.f__Cryomorphaceae.g__Vicingus.s__uncultured_sediment
1205	OTU1205	d__Bacteria.p__Chloroflexi.c__Chloroflexia.oThermomicrobiales...
1226	OTU1226	d__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Rhizobiales.f__Hyphomicrobiaceae.gFilomicrobium.
1228	OTU1228	d__Bacteria.p__Planctomycetota.c__Planctomycetes.o__Pirellulales.f__Pirellulaceae.g__Rhodopirellula.s__uncultured_hydrocarbon
1235	OTU1235	d__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Micavibrionales.f__uncultured.g__uncultured.s__uncultured_organism
1238	OTU1238	d__Bacteria.p__Acidobacteriota.c__Thermoanaerobaculia.o__Thermoanaerobaculales.f__Thermoanaerobaculaceae.g__Subgroup_23.s__uncultured_prokaryote
1240	OTU1240	d__Bacteria.p__Myxococcota.c__Polyangia.o__VHS.B4.70.f__VHS.B4.70.g__VHS.B4.70.s__uncultured_delta
1248	OTU1248	d__Bacteria.p__Planctomycetota.c__Phycisphaerae.o__mle1.8.f__mle1.8.g__mle1.8.s__uncultured_organism
1249	OTU1249	d__Bacteria.p__Myxococcota.c__Polyangia.o__Polyangiales.f__Sandaracinaceae.gSandaracinus.
1250	OTU1250	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Nitrosococcales.f__Nitrosococcaceae.gCI75cm.2.12.
1284	OTU1284	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Steroidobacterales.f__Woeseiaceae.g__JTB255_marine_benthic_group.s__uncultured_organism
1285	OTU1285	d__Bacteria.p__Fibrobacterota.c__Fibrobacteria.o__Fibrobacterales.f__TG3.gTG3.
1287	OTU1287	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__OM182_clade.f__OM182_clade.g__OM182_clade.s__unidentified_marine
1289	OTU1289	d__Bacteria.p__Verrucomicrobiota.c__Lentisphaeria.o__SS1.B.02.17.f__SS1.B.02.17.gSS1.B.02.17.
1298	OTU1298	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Chitinophagales.f__Saprospiraceae.g__uncultured.s__uncultured_Bacteroidetes
1299	OTU1299	d__Bacteria.p__Verrucomicrobiota.c__Kiritimatiellae.o__Kiritimatiellales.f__Kiritimatiellaceae.g__R76.B128.s__Kiritimatiella_sp.
1301	OTU1301	d__Bacteria.p__Fusobacteriota.c__Fusobacteriia.o__Fusobacteriales.f__Fusobacteriaceae.gFusobacterium.
1302	OTU1302	d__Archaea.p__Asgardarchaeota.c__Lokiarchaeia.o__Lokiarchaeia.f__Lokiarchaeia.g__Lokiarchaeia.s__uncultured_crenarchaeote
1303	OTU1303	d__Bacteria.p__Desulfobacterota.c__Desulfuromonadia.o__uncultured.f__uncultured.g__uncultured.s__uncultured_bacterium
1308	OTU1308	d__Bacteria.p__Planctomycetota.c__Phycisphaerae.o__mle1.8.f__mle1.8.gmle1.8.
1310	OTU1310	d__Bacteria.p__Spirochaetota.c__MVP.15.o__MVP.15.f__MVP.15.g__MVP.15.s__uncultured_bacterium
1312	OTU1312	d__Bacteria.p__Campilobacterota.c__Campylobacteria.o__Campylobacterales.f__Sulfurospirillaceae.gSulfurospirillum.
1314	OTU1314	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Nitrosococcales.f__Nitrosococcaceae.g__SZB85.s__uncultured_bacterium
1318	OTU1318	d__Archaea.p__Thermoplasmatota.c__Thermoplasmata.o__Methanomassiliicoccales.f__uncultured.g__uncultured.s__uncultured_euryarchaeote
1321	OTU1321	d__Bacteria.p__Cyanobacteria.c__Cyanobacteriia.o__Cyanobacteriales.f__Xenococcaceae.g__Chroococcidiopsis_PCC.6712.s__uncultured_cyanobacterium
1325	OTU1325	d__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__uncultured.f__uncultured.guncultured.
1329	OTU1329	d__Bacteria.p__Desulfobacterota.c__Desulfobacteria.o__Desulfobacterales.f__Desulfococcaceae.gDesulfonema.
1330	OTU1330	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Thiotrichales.f__Thiotrichaceae..
1338	OTU1338	d__Bacteria.p__Myxococcota.c__Polyangia.o__Blfdi19.f__Blfdi19.g__Blfdi19.s__uncultured_bacterium
1343	OTU1343	d__Bacteria.p__Acidobacteriota.c__Thermoanaerobaculia.o__Thermoanaerobaculales.f__Thermoanaerobaculaceae.g__B276.D12.s__uncultured_bacterium
1347	OTU1347	d__Bacteria.p__Fibrobacterota.c__Chitinivibrionia.o__uncultured.f__uncultured.guncultured.
1350	OTU1350	d__Bacteria.p__Bacteroidota.c__Bacteroidia.o__Flavobacteriales.f__Flavobacteriaceae.gPolaribacter.
1351	OTU1351	d__Bacteria.p__Planctomycetota.c__Phycisphaerae.o__Phycisphaerales.f__AKAU3564_sediment_group.g__AKAU3564_sediment_group.s__uncultured_bacterium
1352	OTU1352	d__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__D90.f__D90.g__D90.s__uncultured_gamma
1353	OTU1353	d__Bacteria.p__Planctomycetota.c__Phycisphaerae.o__Amsterdam.1B.07.f__Amsterdam.1B.07.g__Amsterdam.1B.07.s__uncultured_bacterium
1359	OTU1359	d__Bacteria.p__Patescibacteria.c__Parcubacteria.o__Candidatus_Kaiserbacteria.f__Candidatus_Kaiserbacteria.g__Candidatus_Kaiserbacteria.s__bacterium_SH4.10
1361	OTU1361	d__Bacteria.p__Chloroflexi.c__Anaerolineae.o__Anaerolineales.f__Anaerolineaceae.gPelolinea.
1362	OTU1362	d__Bacteria.p__Gemmatimonadota.c__BD2.11_terrestrial_group.o__BD2.11_terrestrial_group.f__BD2.11_terrestrial_group.g__BD2.11_terrestrial_group.s__unidentified_bacterium
1363	OTU1363	d__Bacteria.p__Sumerlaeota.c__Sumerlaeia.o__uncultured.f__uncultured.g__uncultured.s__uncultured_organism
1369	OTU1369	d__Bacteria.p__Planctomycetota.c__Phycisphaerae.o__Phycisphaerales.f__Phycisphaeraceae.g__uncultured.s__uncultured_bacterium
1370	OTU1370	d__Bacteria.p__Latescibacterota.c__Latescibacterota.o__Latescibacterota.f__Latescibacterota.g__Latescibacterota.s__uncultured_Acidobacterium
1374	OTU1374	d__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Defluviicoccales.f__Defluviicoccaceae.g__Defluviicoccus.s__uncultured_Rhodospirillaceae

The separation between groups is 3.12.

We update the plot with the separations:

intersección=c(dim(Significant.capat)[1],Sep(HC))
Resultados=rbind(Resultados,intersección)
row.names(Resultados)=c(
"LR.max",
"LR.max.local",
"Aldex",
"glmnet",
"glmnet.ext",
"intersection")
colnames(Resultados)=c("Size","Separation")

par(opar)
fit = smooth.spline(F.SS[!is.na(F.SS[,3]),1],F.SS[!is.na(F.SS[,3]),3],cv=TRUE)
fit.low = smooth.spline(F.SS[!is.na(F.SS[,3]),1],F.SS[!is.na(F.SS[,3]),4],cv=TRUE)
fit.up = smooth.spline(F.SS[!is.na(F.SS[,3]),1],F.SS[!is.na(F.SS[,3]),5],cv=TRUE)

plot(F.SS[,c(1,3)],pch=20,cex=0.25,col="darkgrey",xlab="n",ylab="Separation",main="Average separation for perfect classifiers",ylim=c(0,2.25),xlim=c(0,250),xaxp=c(0,250,10),yaxp=c(0,2.5,10))
lines(fit,col="black",lwd=1)
lines(fit.low,col="red",lwd=1)
lines(fit.up,col="red",lwd=1)
points(Resultados,col="blue",type="h")
points(Resultados,col="blue",pch=20)
text(Resultados[,1],Resultados[,2]+0.02,col="blue",labels=row.names(Resultados),cex=0.75)
abline(h=2.47,col="green")
text(20,2.6,col="green",labels="Global",cex=0.75)

Resultados %>%
  kbl() %>%
  kable_styling()

	Size	Separation
LR.max	549	2.829712
LR.max.local	46	4.655234
Aldex	121	3.429094
glmnet	350	2.776603
glmnet.ext	104	4.421816
intersection	312	3.116542

6.5 CAU T2C vs CAU T2HW

tax_otu=as.data.frame(read_excel("TablaOTUs.xlsx"))[1:12,]

Samples=tax_otu$ID 
taxa=colnames(tax_otu[,3:dim(tax_otu)[2]])
OTUs=paste("OTU",1:(dim(tax_otu)[2]-2),sep="")

DF.0=tax_otu[,-c(1,2)]
row.names(DF.0)=Samples
colnames(DF.0)=OTUs

taxa.original=taxa
DF.0.original=DF.0
n.OTUs.original=dim(DF.0)[2]

Miseria=as.vector(which(colSums(DF.0)<=2))
DF.0=DF.0[,-Miseria]
taxa=taxa[-Miseria]
OTUs=OTUs[-Miseria]

hit=function(x){min(c(x,1))}
DF.0.hits=as.matrix(DF.0)
DF.0.hits[]=vapply(DF.0.hits, hit, numeric(1))

Unics=data.frame(
Sample=rep(NA,length(which(colSums(DF.0.hits)==1))), OTUs=names(colSums(DF.0)[which(colSums(DF.0.hits)==1)]), Reads=colSums(DF.0)[which(colSums(DF.0.hits)==1)],
            Proportions=rep(0,length(which(colSums(DF.0.hits)==1)))  
)
for (i in 1:length(Unics$OTUs)){
ii=which(DF.0.hits[,Unics$OTUs[i]]==1)  
Unics$Proportions[i]=DF.0[ii,Unics$OTUs[i]]/sum(DF.0[ii,])
Unics$Sample[i]=Samples[ii]}
Unics.Freqs=Unics[Unics$Proportions>=0.05/100,]
row.names(Unics.Freqs)=NULL


DF.0=DF.0[,-which(colSums(DF.0.hits)==1)]
taxa=taxa[-which(colSums(DF.0.hits)==1)]
OTUs=OTUs[-which(colSums(DF.0.hits)==1)]

row.names(DF.0)=Samples

DF=zCompositions::cmultRepl(DF.0,method="GBM",output="p-counts",suppress.print=TRUE,z.warning=0.99)

DF=DF[7:12,]
DF.0=DF.0[7:12,]
DF.0.original=DF.0.original[7:12 ,]

Type=as.factor(c(rep("CAU_T2C", 3),rep("CAU_T2HW", 3)))
colors=c("purple","red")[Type]

After removing OTUs with 2 or fewer reads across the CAU samples and those appearing in only one of these samples, 1682 taxa remain.

The OTUs removed at this step that represent more than 0.05% of the sample in which they appear are:

Unics.Freqs[rev(order(Unics.Freqs$Proportions)),] %>%
  kbl() %>%
  kable_styling()

	Sample	OTUs	Reads	Proportions
2	CAU_T0_2	OTU966	55	0.0012193
1	CAU_T2HW_1	OTU727	55	0.0008798

rm(tax_otu)
rm(DF.0.hits)
rm(Miseria)
rm(Unics.Freqs)

6.5.1 How different are the samples?

HC=ClusterHC(DF,Grups=Type,colores=colors)

base=Sep(HC)

The two sample types are NOT well separated.

We examine the proportion of OTU subsets of reasonable size that already classify them correctly.

# Fijo una semilla de aleatoriedad para el experimento
> initial_seed=as.integer(Sys.time())
> print (initial_seed)
# [1] 1715851715853234
initial_seed %% 10000
# [1] 3234

set.seed(3234)
Experimento=function(i)
{
  ii=sample(dim(DF)[2],i,rep=FALSE)
  DFtemp=DF[,ii]
  CC=ClusterHC(DFtemp,dendrograma=FALSE,barplot=FALSE, Grups=Type,colores=colors)
  c(Encerts(CC$tabla,table(Type)),Sep(CC))
}
n=500
F.SS=c()
for (i in 10:1000)
  {
  print(i)
  EE=replicate(n,Experimento(i))
  EE.2=EE[2,which(EE[1,]==0)]
  if(length(which(EE[1,]==0))>0){
XX=replicate(1000,mean(sample(EE.2,n,replace=TRUE)))
  F.SS=rbind(F.SS, c(i,
                     length(EE.2)/250,
                      mean(EE.2),
                      quantile(XX,0.025),
                      quantile(XX,0.975)
  ))}
  else {
    F.SS=rbind(F.SS, c(i,
                     0,
                      NA,
                      NA,
                      NA))
  }
  }
colnames(F.SS)=c("n","Proportion","Avg. sep.","Q_0.025","Q_0.975")
saveRDS(F.SS, file="Fraccio.Separadors.CAU.T2CvsT2HW.RData")

F.SS=readRDS("Fraccio.Separadors.CAU.T2CvsT2HW.RData")

The first plot shows, for each \(n\) up to 600, the proportion of samples of size \(n\) that perfectly classify CAU_T2C and CAU_T2HW (black curve), along with the 95% Clopper–Pearson confidence interval for that proportion (red curves). We used smoothing splines to smooth the curves.

F.SS_prop.Q_0.025=epitools::binom.exact(F.SS[,2]*250,250)$lower
F.SS_prop.Q_0.975=epitools::binom.exact(F.SS[,2]*250,250)$upper
fit = smooth.spline(F.SS[,1],F.SS[,2],cv=TRUE)
fit.low = smooth.spline(F.SS[,1],F.SS_prop.Q_0.025,cv=TRUE)
fit.up = smooth.spline(F.SS[,1],F.SS_prop.Q_0.975,cv=TRUE)


plot(F.SS[,1:2],pch=20,cex=0.25,col="darkgrey",xlab="n",ylab="Proportion",main="Proportion of perfect classifiers",ylim=c(0,0.1),xlim=c(0,600),xaxp=c(0,600,12),yaxp=c(0,0.1,10))
lines(fit,col="black",lwd=1)
lines(fit.low,col="red",lwd=1)
lines(fit.up,col="red",lwd=1)

The second plot shows, for each \(n\) up to 600, the estimated mean separation obtained with a sample of size \(n\) that perfectly classifies CAU_T2C and CAU_T2HW (black curve), along with the 95% confidence interval of this mean separation obtained via bootstrap (red curve). Note that from \(n=350\) onward, NO subset is found that separates the two groups.

fit = smooth.spline(F.SS[!is.na(F.SS[,3]),1],F.SS[!is.na(F.SS[,3]),3],cv=TRUE)
fit.low = smooth.spline(F.SS[!is.na(F.SS[,3]),1],F.SS[!is.na(F.SS[,3]),4],cv=TRUE)
fit.up = smooth.spline(F.SS[!is.na(F.SS[,3]),1],F.SS[!is.na(F.SS[,3]),5],cv=TRUE)

plot(F.SS[,c(1,3)],pch=20,cex=0.25,col="darkgrey",xlab="n",ylab="Separation",main="Average separation for perfect classifiers",xlim=c(0,600),xaxp=c(0,600,12),yaxp=c(0,1.5,15))
lines(fit,col="black",lwd=1)
lines(fit.low,col="red",lwd=1)
lines(fit.up,col="red",lwd=1)

`

6.5.2 Taxa with maximum relevant log-ratios

LRS=explore_logratios(DF,Type)
saveRDS(LRS, file="LRS_CAU_2C2HW.RData")

LRS=readRDS("LRS_CAU_2C2HW.RData")

assoc=rep(0,dim(DF)[2]-4)
for (m in 5:dim(DF)[2]){
    assoc[m-4]=sum(LRS$`association log-ratio with y`[1:m,1:m])/m^2
}
saveRDS(assoc, file="assoc_CAU_2C2HW.RData")

assoc=readRDS("assoc_CAU_2C2HW.RData")
plot(5:dim(DF)[2],assoc,type="b",xlab="m",ylab="Average goodness of the m most relevant." ,pch=20,cex=0.5)

m=4+which.max(assoc)
impLR=sort(as.numeric(LRS$`order of importance`[1:m]))

HC=ClusterHC(DF[,impLR],barplot=FALSE,Grups=Type,colores=colors)

LR.max=c(length(impLR),Sep(HC))

The maximum is attained at the set of 95 most logratio-relevant taxa.
They perfectly separate the two sample types. The separation between groups is 1.98.

Significant=data.frame(
  OTUs=paste("OTU",1:n.OTUs.original,sep=""),
  taxa=taxa.original,
  Log_ratio.max=Indicador(impLR))

6.5.3 Taxa relevant for the bacterial signature (according to coda_glmnet)

coda.glmnet=coda_glmnet(DF,Type,showPlots = FALSE)

## [1] "No variables are selected. The prediction and the signature plots are not displayed."

coda.glmnet$`signature plot`

## NULL

coda_glmnet does not find taxa with significant differences, likely due to the low power with only 3 vs. 3 samples. When this happens, we add random replicates, with the idea that stochastic resonance may strengthen the signal. We test with 3, 5, and 10 replicates.

> initial_seed=as.integer(Sys.time())
> print (initial_seed)
# [1] 1711435693
initial_seed %% 10000
# [1] 5693

# 3 replicates
set.seed(5693)
M=3
repls=aldexCesc.clr(t(DF), conds=Type, mc.samples=M)@analysisData

## [1] "operating in serial mode"

repls=t(cbind(repls$CAU_T2C_1,repls$CAU_T2C_2,repls$CAU_T2C_3,repls$CAU_T2HW_1,repls$CAU_T2HW_2,repls$CAU_T2HW_3))
attr(repls,"dimnames")[[2]]=NULL
colnames(repls)=colnames(DF)
row.names(repls)=c(paste("CAU_T2C_1",1:M,sep="_"),
  paste("CAU_T2C_2",1:M,sep="_"),
  paste("CAU_T2C_3",1:M,sep="_"),
  paste("CAU_T2HW_1",1:M,sep="_"),
  paste("CAU_T2HW_2",1:M,sep="_"),
  paste("CAU_T2HW_3",1:M,sep="_"))
mostres=rbind(repls,easyCODA::CLR(DF)$LR)
rm(repls)
Type_ext=as.factor(c(rep("CAU_T2C", 3*M),rep("CAU_T2HW", 3*M),rep("CAU_T2C", 3),rep("CAU_T2HW", 3)))
colors_ext=c("purple","red")[Type_ext]

LogRat_mostres=logratios_matrix_clr(mostres)
saveRDS(LogRat_mostres, file="LogRat_mostres_CAU_2C2HW_3copies.RData")

LogRat_mostres=readRDS("LogRat_mostres_CAU_2C2HW_3copies.RData")
LogRat_mostres=list(LogRat_mostres[[1]],LogRat_mostres[[2]])

coda.glmnet.3=coda_glmnet_lr_bin(LogRat_mostres,Type_ext,taxa,showPlots = FALSE)

impGLMNET_ext.3=coda.glmnet.3$taxa.num
HC=ClusterHC(DF[,impGLMNET_ext.3],dendrograma=TRUE,barplot=FALSE,Grups=Type,colores=colors)

glmnet.ext.3=c(length(impGLMNET_ext.3),Sep(HC))

With 3 replicates, 42 significant taxa are found, perfectly separating the two groups, with a separation of 1.49.

# 5 replicates
set.seed(5693)
M=5
repls=aldexCesc.clr(t(DF), conds=Type, mc.samples=M)@analysisData

## [1] "operating in serial mode"

repls=t(cbind(repls$CAU_T2C_1,repls$CAU_T2C_2,repls$CAU_T2C_3,repls$CAU_T2HW_1,repls$CAU_T2HW_2,repls$CAU_T2HW_3))
attr(repls,"dimnames")[[2]]=NULL
colnames(repls)=colnames(DF)
row.names(repls)=c(paste("CAU_T2C_1",1:M,sep="_"),
  paste("CAU_T2C_2",1:M,sep="_"),
  paste("CAU_T2C_3",1:M,sep="_"),
  paste("CAU_T2HW_1",1:M,sep="_"),
  paste("CAU_T2HW_2",1:M,sep="_"),
  paste("CAU_T2HW_3",1:M,sep="_"))
mostres=rbind(repls,easyCODA::CLR(DF)$LR)
rm(repls)
Type_ext=as.factor(c(rep("CAU_T2C", 3*M),rep("CAU_T2HW", 3*M),rep("CAU_T2C", 3),rep("CAU_T2HW", 3)))
colors_ext=c("purple","red")[Type_ext]

LogRat_mostres=logratios_matrix_clr(mostres)
saveRDS(LogRat_mostres, file="LogRat_mostres_CAU_2C2HW_5copies.RData")

LogRat_mostres=readRDS("LogRat_mostres_CAU_2C2HW_5copies.RData")
LogRat_mostres=list(LogRat_mostres[[1]],LogRat_mostres[[2]])

coda.glmnet.5=coda_glmnet_lr_bin(LogRat_mostres,Type_ext,taxa,showPlots = FALSE)

impGLMNET_ext.5=coda.glmnet.5$taxa.num
HC=ClusterHC(DF[,impGLMNET_ext.5],dendrograma=TRUE,barplot=FALSE,Grups=Type,colores=colors)

glmnet.ext.5=c(length(impGLMNET_ext.5),Sep(HC))

With 5 replicates, 53 significant taxa are found, perfectly separating the two groups, with a separation of 1.2.

Significant=cbind(Significant,
glmnet_sign.ext.5.T2C=Indicador(coda.glmnet.5$taxa.num[coda.glmnet.5$`log-contrast coefficients`>0]),
glmnet_sign.ext.5.T2HW=Indicador(coda.glmnet.5$taxa.num[coda.glmnet.5$`log-contrast coefficients`<0]))

set.seed(5693)
M=10
repls=aldexCesc.clr(t(DF), conds=Type, mc.samples=M)@analysisData

## [1] "operating in serial mode"

repls=t(cbind(repls$CAU_T2C_1,repls$CAU_T2C_2,repls$CAU_T2C_3,repls$CAU_T2HW_1,repls$CAU_T2HW_2,repls$CAU_T2HW_3))
attr(repls,"dimnames")[[2]]=NULL
colnames(repls)=colnames(DF)
row.names(repls)=c(paste("CAU_T2C_1",1:M,sep="_"),
  paste("CAU_T2C_2",1:M,sep="_"),
  paste("CAU_T2C_3",1:M,sep="_"),
  paste("CAU_T2HW_1",1:M,sep="_"),
  paste("CAU_T2HW_2",1:M,sep="_"),
  paste("CAU_T2HW_3",1:M,sep="_"))
mostres=rbind(repls,easyCODA::CLR(DF)$LR)
rm(repls)
Type_ext=as.factor(c(rep("CAU_T2C", 3*M),rep("CAU_T2HW", 3*M),rep("CAU_T2C", 3),rep("CAU_T2HW", 3)))
colors_ext=c("purple","red")[Type_ext]

LogRat_mostres=logratios_matrix_clr(mostres)
saveRDS(LogRat_mostres, file="LogRat_mostres_CAU_2C2HW_10copies.RData")

LogRat_mostres=readRDS("LogRat_mostres_CAU_2C2HW_10copies.RData")
LogRat_mostres=list(LogRat_mostres[[1]],LogRat_mostres[[2]])

coda.glmnet.10=coda_glmnet_lr_bin(LogRat_mostres,Type_ext,taxa,showPlots = FALSE)

impGLMNET_ext.10=coda.glmnet.10$taxa.num
HC=ClusterHC(DF[,impGLMNET_ext.10],dendrograma=TRUE,barplot=FALSE,Grups=Type,colores=colors)

glmnet.ext.10=c(length(impGLMNET_ext.10),Sep(HC))

With 10 replicates, 59 significant taxa are found, perfectly separating the two groups, with a separation of 1.12.

Significant=cbind(Significant,
glmnet_sign.ext.10.T2C=Indicador(coda.glmnet.10$taxa.num[coda.glmnet.10$`log-contrast coefficients`>0]),
glmnet_sign.ext.10.T2HW=Indicador(coda.glmnet.10$taxa.num[coda.glmnet.10$`log-contrast coefficients`<0]))

6.5.4 OTUs significant according to ALDeX

> initial_seed=as.integer(Sys.time())
> print (initial_seed)
# [1] 1711461735
initial_seed %% 10000
# [1] 1735

set.seed(1735)
repl_kw=aldexCesc.clr(t(DF), conds=Type, mc.samples=1000, verbose=FALSE)
aldex_kw=aldex.kw(repl_kw, verbose=FALSE)
#
saveRDS(repl_kw, file="repl_kw_CAU_2C2HW.RData")
saveRDS(aldex_kw, file="aldex_kw_CAU_2C2HW.RData")

p.valores_kw=readRDS("aldex_kw_CAU_2C2HW.RData") 

min(p.valores_kw[,1])

## [1] 0.04999719

min(p.valores_kw[,2])

## [1] 0.3641574

min(p.valores_kw[,3])

## [1] 0.002010094

min(p.valores_kw[,4])

## [1] 0.07355742

length(p.valores_kw[p.valores_kw[,3]<0.01,2])

## [1] 11

length(p.valores_kw[p.valores_kw[,3]<0.05,2])

## [1] 68

There are no taxa with even an unadjusted p-value < 0.05.

6.5.5 Simper

DF.prop=DF.0.original/rowSums(DF.0.original)
SMP.prop=simper(DF.prop,group=Type)
indexos_SMP.07=SMP.prop$CAU_T2C_CAU_T2HW$ord[which(SMP.prop$CAU_T2C_CAU_T2HW$cusum<=0.7)]
indexos_SMP.05=SMP.prop$CAU_T2C_CAU_T2HW$ord[which(SMP.prop$CAU_T2C_CAU_T2HW$cusum<=0.5)]

OTUs_SMP.07=sort(attr(SMP.prop$CAU_T2C_CAU_T2HW$cusum[which(SMP.prop$CAU_T2C_CAU_T2HW$cusum<=0.7)],"names"))
OTUs_SMP.good.07=setdiff(OTUs_SMP.07,Unics$OTUs)

simper identifies 170 significant taxa, but they do not separate the samples well.

HC=ClusterHC(DF[,OTUs_SMP.good.07],dendrograma=TRUE,barplot=FALSE,Grups=Type,colores=colors)

Significant=cbind(Significant,
t(DF.prop))

6.5.6 Summary

write.csv2(Significant,"OTU_Significativos_CAU_T2.csv",row.names=FALSE)

Resultados=rbind(
LR.max,
glmnet.ext.3,
glmnet.ext.5,
glmnet.ext.10

)
row.names(Resultados)=c(
"LR",
"glmnet.ext.3",
"glmnet.ext.5",
"glmnet.ext.10")
colnames(Resultados)=c("Size","Separation")

fit = smooth.spline(F.SS[!is.na(F.SS[,3]),1],F.SS[!is.na(F.SS[,3]),3],cv=TRUE)
fit.low = smooth.spline(F.SS[!is.na(F.SS[,3]),1],F.SS[!is.na(F.SS[,3]),4],cv=TRUE)
fit.up = smooth.spline(F.SS[!is.na(F.SS[,3]),1],F.SS[!is.na(F.SS[,3]),5],cv=TRUE)

plot(F.SS[,c(1,3)],pch=20,cex=0.25,col="darkgrey",xlab="n",ylab="Separation",main="Average separation for perfect classifiers",ylim=c(0,2.25),xlim=c(0,250),xaxp=c(0,250,10),yaxp=c(0,2.5,10))
lines(fit,col="black",lwd=1)
lines(fit.low,col="red",lwd=1)
lines(fit.up,col="red",lwd=1)

points(Resultados,col="blue",type="h")
points(Resultados,col="blue",pch=20)
text(Resultados[,1],Resultados[,2]+0.02,col="blue",labels=row.names(Resultados),cex=0.75)

Finally, we intersect the OTUs identified as significant according to LR and coda_glmnet with 3 replicates

Significant.capat=Significant[,c(1,2,3,4,5)]
Significant.capat=cbind(Significant.capat,Cuánto=rowSums(Significant.capat[,3:dim(Significant.capat)[2]]))
Significant.capat=Significant.capat[Significant.capat$Cuánto==2,]

DF.Imp=DF[,Significant.capat[,1]]
HC=ClusterHC(DF.Imp,dendrograma=TRUE,barplot=FALSE,Grups=Type,colores=colors)

There are 10 taxa. They are:

Significant.capat[,1:2]%>%
  kbl() %>%
  kable_styling() 

	OTUs	taxa
OTU38	OTU38	Unassigned;;;;;;
OTU108	OTU108	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Spirochaetales;f__Spirochaetaceae;gGWE2-31-10;
OTU199	OTU199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Oceanospirillales;f__Halomonadaceae;gCobetia;
OTU208	OTU208	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;gLutibacter;
OTU337	OTU337	d__Bacteria;p__Chloroflexi;c__Anaerolineae;o__SJA-15;f__SJA-15;g__SJA-15;s__uncultured_Chloroflexi
OTU365	OTU365	d__Bacteria;p__Firmicutes;c__Clostridia;oLachnospirales;;;
OTU383	OTU383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Alteromonadales;f__Alteromonadaceae;;
OTU685	OTU685	d__Bacteria;p__PAUC34f;c__PAUC34f;o__PAUC34f;f__PAUC34f;g__PAUC34f;s__uncultured_bacterium
OTU708	OTU708	d__Bacteria;p__Patescibacteria;c__Gracilibacteria;o__Gracilibacteria;f__Gracilibacteria;g__Gracilibacteria;s__uncultured_organism
OTU1120	OTU1120	d__Bacteria;p__Calditrichota;c__Calditrichia;o__Calditrichales;f__Calditrichaceae;gCaldithrix;

The separation between groups is 1.96.

We update the plot with the separations:

intersección=c(dim(Significant.capat)[1],Sep(HC))
Resultados=rbind(Resultados,intersección)
row.names(Resultados)=c(
"LR",
"glmnet.ext.3",
"glmnet.ext.5",
"glmnet.ext.10",
"intersection")
colnames(Resultados)=c("Size","Separation")

par(opar)
fit = smooth.spline(F.SS[!is.na(F.SS[,3]),1],F.SS[!is.na(F.SS[,3]),3],cv=TRUE)
fit.low = smooth.spline(F.SS[!is.na(F.SS[,3]),1],F.SS[!is.na(F.SS[,3]),4],cv=TRUE)
fit.up = smooth.spline(F.SS[!is.na(F.SS[,3]),1],F.SS[!is.na(F.SS[,3]),5],cv=TRUE)

plot(F.SS[,c(1,3)],pch=20,cex=0.25,col="darkgrey",xlab="n",ylab="Separation",main="Average separation for perfect classifiers",ylim=c(0,2.25),xlim=c(0,250),xaxp=c(0,250,10),yaxp=c(0,2.5,10))
lines(fit,col="black",lwd=1)
lines(fit.low,col="red",lwd=1)
lines(fit.up,col="red",lwd=1)
points(Resultados,col="blue",type="h")
points(Resultados,col="blue",pch=20)
text(Resultados[,1],Resultados[,2]+0.02,col="blue",labels=row.names(Resultados),cex=0.75)
abline(h=2.47,col="green")
text(20,2.6,col="green",labels="Global",cex=0.75)

Resultados %>%
  kbl() %>%
  kable_styling()

	Size	Separation
LR	95	1.981986
glmnet.ext.3	42	1.492428
glmnet.ext.5	53	1.203924
glmnet.ext.10	59	1.120839
intersection	10	1.960728

6.6 CYM T2C vs CYM T2HW

tax_otu=as.data.frame(read_excel("TablaOTUs.xlsx"))[13:24,]
Samples=tax_otu$ID 
taxa=colnames(tax_otu[,3:dim(tax_otu)[2]])
OTUs=paste("OTU",1:(dim(tax_otu)[2]-2),sep="")

DF.0=tax_otu[,-c(1,2)]
row.names(DF.0)=Samples
colnames(DF.0)=OTUs

taxa.original=taxa
DF.0.original=DF.0
n.OTUs.original=dim(DF.0)[2]
indices=1:n.OTUs.original

hit=function(x){min(c(x,1))}
DF.0.hits=as.matrix(DF.0)
DF.0.hits[]=vapply(DF.0.hits, hit, numeric(1))

Unics=data.frame(
Sample=rep(NA,length(which(colSums(DF.0.hits)==1))), OTUs=names(colSums(DF.0)[which(colSums(DF.0.hits)==1)]), Reads=colSums(DF.0)[which(colSums(DF.0.hits)==1)],
            Proportions=rep(0,length(which(colSums(DF.0.hits)==1)))  
)
for (i in 1:length(Unics$OTUs)){
ii=which(DF.0.hits[,Unics$OTUs[i]]==1)  
Unics$Proportions[i]=DF.0[ii,Unics$OTUs[i]]/sum(DF.0[ii,])
Unics$Sample[i]=Samples[ii]}
Unics.Freqs=Unics[Unics$Proportions>=0.05/100,]
row.names(Unics.Freqs)=NULL

Miseria=as.vector(which(colSums(DF.0)<=2|colSums(DF.0.hits)==1))
DF.0=DF.0[,-Miseria]
taxa=taxa[-Miseria]
OTUs=OTUs[-Miseria]
indices=indices[-Miseria]

row.names(DF.0)=Samples

DF=zCompositions::cmultRepl(DF.0,method="GBM",output="p-counts",suppress.print=TRUE,z.warning=0.99)

DF.0=DF.0[7:12,]
DF=DF[7:12,]
DF.0.original=DF.0.original[7:12 ,]

Type=as.factor(c(rep("CYM_T2C", 3),rep("CYM_T2HW", 3)))
colors=c("purple","red")[Type]

After removing OTUs with 2 or fewer reads across the CAU samples and those appearing in only one of these samples, 2247 taxa remain.

The OTUs removed at this step that represent more than 0.05% of the sample in which they appear are:

Unics.Freqs[rev(order(Unics.Freqs$Proportions)),] %>%
  kbl() %>%
  kable_styling()

Sample	OTUs	Reads	Proportions
CYM_T2C_1	OTU2121	186	0.0020402

rm(tax_otu)
rm(DF.0.hits)
rm(Miseria)
rm(Unics.Freqs)

6.6.1 How different are the samples?

HC=ClusterHC(DF,Grups=Type,colores=colors)

base=Sep(HC)

The two sample types are perfectly separated from the start. The separation between groups is 1.21.

We examine the proportion of OTU subsets of reasonable size that already classify them correctly.

> initial_seed=as.integer(Sys.time())
> print (initial_seed)
# [1] 1714640507
initial_seed %% 10000
# [1] 507

set.seed(507)
Experimento=function(i)
{
  ii=sample(dim(DF)[2],i,rep=FALSE)
  DFtemp=DF[,ii]
  CC=ClusterHC(DFtemp,dendrograma=FALSE,barplot=FALSE, Grups=Type,colores=colors)
  c(Encerts(CC$tabla,table(Type)),Sep(CC))
}
n=250
F.SS=c()
for (i in 10:1000)
  {
  print(i)
  EE=replicate(n,Experimento(i))
  EE.2=EE[2,which(EE[1,]==0)]
XX=replicate(1000,mean(sample(EE.2,n,replace=TRUE)))
  F.SS=rbind(F.SS, c(i,
                     length(EE.2)/250,
                      mean(EE.2),
                      quantile(XX,0.025),
                      quantile(XX,0.975)
  ))
  }
colnames(F.SS)=c("n","Proportion","Avg. sep.","Q_0.025","Q_0.975")
saveRDS(F.SS, file="Fraccio.Separadors.CYM.T2CvsT2HW.RData")

F.SS=readRDS("Fraccio.Separadors.CYM.T2CvsT2HW.RData")

The first plot shows, for each \(n\) up to 600, the proportion of samples of size \(n\) that perfectly classify CYM_T2C and CYM_T2HW (black curve), along with the 95% Clopper–Pearson confidence interval for that proportion (red curves). We used smoothing splines to smooth the curves.

F.SS_prop.Q_0.025=epitools::binom.exact(F.SS[,2]*250,250)$lower
F.SS_prop.Q_0.975=epitools::binom.exact(F.SS[,2]*250,250)$upper
fit = smooth.spline(F.SS[,1],F.SS[,2],cv=TRUE)
fit.low = smooth.spline(F.SS[,1],F.SS_prop.Q_0.025,cv=TRUE)
fit.up = smooth.spline(F.SS[,1],F.SS_prop.Q_0.975,cv=TRUE)


plot(F.SS[,1:2],pch=20,cex=0.25,col="darkgrey",xlab="n",ylab="Proportion",main="Proportion of perfect classifiers",xlim=c(0,1000),xaxp=c(0,1000,20),yaxp=c(0,1,10))
lines(fit,col="black",lwd=1)
lines(fit.low,col="red",lwd=1)
lines(fit.up,col="red",lwd=1)

The second plot shows, for each \(n\) up to 600, the estimated mean separation obtained with a sample of size \(n\) that perfectly classifies CYM_T2C and CYM_T2HW (black curve), along with the 95% confidence interval of this mean separation obtained via bootstrap (red curve).

fit = smooth.spline(F.SS[,1],F.SS[,3],cv=TRUE)
fit.low = smooth.spline(F.SS[,1],F.SS[,4],cv=TRUE)
fit.up = smooth.spline(F.SS[,1],F.SS[,5],cv=TRUE)

plot(F.SS[,c(1,3)],pch=20,cex=0.25,col="darkgrey",xlab="n",ylab="Separation",main="Average separation for perfect classifiers",xlim=c(0,1000),xaxp=c(0,1000,20),yaxp=c(0,2.5,10))
lines(fit,col="black",lwd=1)
lines(fit.low,col="red",lwd=1)
lines(fit.up,col="red",lwd=1)
abline(h=base,col="green")

`

6.6.2 Taxa with maximum relevant log-ratios

LRS=explore_logratios(DF,Type)
saveRDS(LRS, file="LRS_CYM_2C2HW.RData")

LRS=readRDS("LRS_CYM_2C2HW.RData")

assoc=rep(0,dim(DF)[2]-4)
for (m in 5:dim(DF)[2]){
    assoc[m-4]=sum(LRS$`association log-ratio with y`[1:m,1:m])/m^2
}
saveRDS(assoc, file="assoc_CYM_2C2HW.RData")

assoc=readRDS("assoc_CYM_2C2HW.RData")
plot(5:dim(DF)[2],assoc,type="b",xlab="m",ylab="Average goodness of the m most relevant." ,pch=20,cex=0.5)

m=4+which.max(assoc)
impLR=sort(as.numeric(LRS$`order of importance`[1:m]))

HC=ClusterHC(DF[,impLR],barplot=FALSE,Grups=Type,colores=colors)

LR.max=c(length(impLR),Sep(HC))

The maximum is attained at the set of 563 most logratio-relevant taxa.
They perfectly separate the two sample types. The separation between groups is 2.15.

Significant=data.frame(
  OTUs=paste("OTU",1:n.OTUs.original,sep=""),
  taxa=taxa.original,
  Log_ratio.max=Indicador(impLR)
  )

6.6.3 Taxa relevant for the bacterial signature (according to coda_glmnet)

coda.glmnet=coda_glmnet(DF,Type,showPlots = FALSE)

## [1] "No variables are selected. The prediction and the signature plots are not displayed."

coda.glmnet$`signature plot`

## NULL

coda_glmnet does not find taxa with significant differences. We add random replicates. We test with 3, 5, and 10 replicates.

# 3 replicates
set.seed(5693)
M=3
repls=aldexCesc.clr(t(DF), conds=Type, mc.samples=M)@analysisData

## [1] "operating in serial mode"

repls=t(cbind(repls$CYM_T2C_1,repls$CYM_T2C_2,repls$CYM_T2C_3,repls$CYM_T2HW_1,repls$CYM_T2HW_2,repls$CYM_T2HW_3))
attr(repls,"dimnames")[[2]]=NULL
colnames(repls)=colnames(DF)
row.names(repls)=c(paste("CYM_T2C_1",1:M,sep="_"),
  paste("CYM_T2C_2",1:M,sep="_"),
  paste("CYM_T2C_3",1:M,sep="_"),
  paste("CYM_T2HW_1",1:M,sep="_"),
  paste("CYM_T2HW_2",1:M,sep="_"),
  paste("CYM_T2HW_3",1:M,sep="_"))
mostres=rbind(repls,easyCODA::CLR(DF)$LR)
rm(repls)
Type_ext=as.factor(c(rep("CYM_T2C", 3*M),rep("CYM_T2HW", 3*M),rep("CYM_T2C", 3),rep("CYM_T2HW", 3)))
colors_ext=c("purple","red")[Type_ext]

LogRat_mostres=logratios_matrix_clr(mostres)
saveRDS(LogRat_mostres, file="LogRat_mostres_CYM_2C2HW_3copies.RData")

LogRat_mostres=readRDS("LogRat_mostres_CYM_2C2HW_3copies.RData")
LogRat_mostres=list(LogRat_mostres[[1]],LogRat_mostres[[2]])

coda.glmnet.3=coda_glmnet_lr_bin(LogRat_mostres,Type_ext,taxa,showPlots = FALSE)

impGLMNET_ext.3=coda.glmnet.3$taxa.num
HC=ClusterHC(DF[,impGLMNET_ext.3],dendrograma=TRUE,barplot=FALSE,Grups=Type,colores=colors)

glmnet.ext.3=c(length(impGLMNET_ext.3),Sep(HC))

With 3 replicates, 81 significant taxa are found, perfectly separating the two groups, with a separation of 3.67.

Significant=cbind(Significant,
glmnet_sign.ext.3.T2C=Indicador(coda.glmnet.3$taxa.num[coda.glmnet.3$`log-contrast coefficients`>0]),
glmnet_sign.ext.3.T2HW=Indicador(coda.glmnet.3$taxa.num[coda.glmnet.3$`log-contrast coefficients`<0]))

# 5 replicates
set.seed(5693)
M=5
repls=aldexCesc.clr(t(DF), conds=Type, mc.samples=M)@analysisData

## [1] "operating in serial mode"

repls=t(cbind(repls$CYM_T2C_1,repls$CYM_T2C_2,repls$CYM_T2C_3,repls$CYM_T2HW_1,repls$CYM_T2HW_2,repls$CYM_T2HW_3))
attr(repls,"dimnames")[[2]]=NULL
colnames(repls)=colnames(DF)
row.names(repls)=c(paste("CYM_T2C_1",1:M,sep="_"),
  paste("CYM_T2C_2",1:M,sep="_"),
  paste("CYM_T2C_3",1:M,sep="_"),
  paste("CYM_T2HW_1",1:M,sep="_"),
  paste("CYM_T2HW_2",1:M,sep="_"),
  paste("CYM_T2HW_3",1:M,sep="_"))
mostres=rbind(repls,easyCODA::CLR(DF)$LR)
rm(repls)
Type_ext=as.factor(c(rep("CYM_T2C", 3*M),rep("CYM_T2HW", 3*M),rep("CYM_T2C", 3),rep("CYM_T2HW", 3)))
colors_ext=c("purple","red")[Type_ext]

LogRat_mostres=logratios_matrix_clr(mostres)
saveRDS(LogRat_mostres, file="LogRat_mostres_CYM_2C2HW_5copies.RData")

LogRat_mostres=readRDS("LogRat_mostres_CYM_2C2HW_5copies.RData")
LogRat_mostres[[1]]=LogRat_mostres[[1]][c(1:30,37:42),]
LogRat_mostres=list(LogRat_mostres[[1]],LogRat_mostres[[2]])

coda.glmnet.5=coda_glmnet_lr_bin(LogRat_mostres,Type_ext,taxa,showPlots = FALSE)

impGLMNET_ext.5=coda.glmnet.5$taxa.num
HC=ClusterHC(DF[,impGLMNET_ext.5],dendrograma=TRUE,barplot=FALSE,Grups=Type,colores=colors)

glmnet.ext.5=c(length(impGLMNET_ext.5),Sep(HC))

With 5 replicates, 84 significant taxa are found, perfectly separating the two groups, with a separation of 3.4.

Significant=cbind(Significant,
glmnet_sign.ext.5.T2C=Indicador(coda.glmnet.5$taxa.num[coda.glmnet.5$`log-contrast coefficients`>0]),
glmnet_sign.ext.5.T2HW=Indicador(coda.glmnet.5$taxa.num[coda.glmnet.5$`log-contrast coefficients`<0]))

set.seed(5693)
M=10
repls=aldexCesc.clr(t(DF), conds=Type, mc.samples=M)@analysisData

## [1] "operating in serial mode"

repls=t(cbind(repls$CYM_T2C_1,repls$CYM_T2C_2,repls$CYM_T2C_3,repls$CYM_T2HW_1,repls$CYM_T2HW_1,repls$CYM_T2HW_3))
attr(repls,"dimnames")[[2]]=NULL
colnames(repls)=colnames(DF)
row.names(repls)=c(paste("CYM_T2C_1",1:M,sep="_"),
  paste("CYM_T2C_2",1:M,sep="_"),
  paste("CYM_T2C_3",1:M,sep="_"),
  paste("CYM_T2HW_1",1:M,sep="_"),
  paste("CYM_T2HW_2",1:M,sep="_"),
  paste("CYM_T2HW_3",1:M,sep="_"))
mostres=rbind(repls,easyCODA::CLR(DF)$LR)
rm(repls)
Type_ext=as.factor(c(rep("CYM_T2C", 3*M),rep("CYM_T2HW", 3*M),rep("CYM_T2C", 3),rep("CYM_T2HW", 3)))
colors_ext=c("purple","red")[Type_ext]

LogRat_mostres=logratios_matrix_clr(mostres)
saveRDS(LogRat_mostres, file="LogRat_mostres_CYM_2C2HW_10copies.RData")

LogRat_mostres=readRDS("LogRat_mostres_CYM_2C2HW_10copies.RData")
LogRat_mostres[[1]]=LogRat_mostres[[1]][c(1:60,67:72),]
LogRat_mostres=list(LogRat_mostres[[1]],LogRat_mostres[[2]])

coda.glmnet.10=coda_glmnet_lr_bin(LogRat_mostres,Type_ext,taxa,showPlots = FALSE)

impGLMNET_ext.10=coda.glmnet.10$taxa.num
HC=ClusterHC(DF[,impGLMNET_ext.10],dendrograma=TRUE,barplot=FALSE,Grups=Type,colores=colors)

glmnet.ext.10=c(length(impGLMNET_ext.10),Sep(HC))

With 10 replicates, 82 significant taxa are found, perfectly separating the two groups, with a separation of 3.09.

Significant=cbind(Significant,
glmnet_sign.ext.10.T2C=Indicador(coda.glmnet.10$taxa.num[coda.glmnet.10$`log-contrast coefficients`>0]),
glmnet_sign.ext.10.T2HW=Indicador(coda.glmnet.10$taxa.num[coda.glmnet.10$`log-contrast coefficients`<0]))

6.6.4 OTUs significant according to ALDeX

> initial_seed=as.integer(Sys.time())
> print (initial_seed)
# [1] 1711815195
initial_seed %% 10000
# [1] 5195

set.seed(5195)
repl_kw=aldexCesc.clr(t(DF), Type=Type, mc.samples=1000, verbose=FALSE)
aldex_kw=aldex.kw(repl_kw, verbose=FALSE)
#
saveRDS(repl_kw, file="repl_kw_2C2HW.RData")
saveRDS(aldex_kw, file="aldex_kw_2C2HW.RData")

p.valores_kw=readRDS("aldex_kw_2C2HW.RData") 

length(p.valores_kw[p.valores_kw[,1]<0.01,1])

## [1] 0

length(p.valores_kw[p.valores_kw[,1]<0.05,1])

## [1] 29

length(p.valores_kw[p.valores_kw[,2]<0.01,2])

## [1] 0

length(p.valores_kw[p.valores_kw[,2]<0.01,2])

## [1] 0

sep.kw.noadjust.0.05=QQ.HC.noadjust(p.valores_kw,DF,Type,q=0.05,1,BP=TRUE)

There are no taxa with a Kruskal–Wallis adjusted p-value < 0.05. There are 29 with an unadjusted p-value < 0.05 (none < 0.01); in the absence of a better option, we select them. They perfectly separate the two groups, with a separation of 3.11.

Significant=cbind(Significant,
Aldex.kw.noadjust.0.05=Indicador(sep.kw.noadjust.0.05))

6.7 Simper

DF.prop=DF.0.original/rowSums(DF.0.original)
SMP.prop=simper(DF.prop,group=Type)
indexos_SMP=SMP.prop$CYM_T2C_CYM_T2HW$ord[which(SMP.prop$CYM_T2C_CYM_T2HW$cusum<=0.7)]
OTUs_SMP=sort(attr(SMP.prop$CYM_T2C_CYM_T2HW$cusum[which(SMP.prop$CYM_T2C_CYM_T2HW$cusum<=0.7)],"names"))
OTUs_SMP.good=setdiff(OTUs_SMP,Unics$OTUs)
HC=ClusterHC(DF[,OTUs_SMP.good],dendrograma=TRUE,barplot=FALSE,Grups=Type,colores=colors)
simper.props=c(length(indexos_SMP),Sep(HC))

We obtain 120 significant taxa, which perfectly separate the two sample types.They include OTU2121, which we had previously removed because it appeared in only one sample. The separation between groups is 1.42.

Indicador.Gl=function(x,k=n.OTUs.original){
  xx=rep(0,k)
 xx[x]=1
  return(xx)
}
Significant=cbind(Significant,
simper.rel=Indicador.Gl(indexos_SMP))
Significant=cbind(Significant,
t(DF.prop))

6.7.1 Summary

write.csv2(Significant,"OTU_Significativos_CYM_T2.csv",row.names=FALSE)

Resultados=rbind(
LR.max,
glmnet.ext.3,
glmnet.ext.5,
glmnet.ext.10,
sep.kw.noadjust.0.05,
simper.props
)
row.names(Resultados)=c(
"LR",
"glmnet.ext.3",
"glmnet.ext.5",
"glmnet.ext.10",
"Aldex",
"simper")
colnames(Resultados)=c("Size","Separation")

par(opar)
fit = smooth.spline(F.SS[,1],F.SS[,3],cv=TRUE)
fit.low = smooth.spline(F.SS[,1],F.SS[,4],cv=TRUE)
fit.up = smooth.spline(F.SS[,1],F.SS[,5],cv=TRUE)

plot(F.SS[,c(1,3)],pch=20,cex=0.25,col="darkgrey",xlab="n",ylab="Separation",main="Average separation for perfect classifiers",xlim=c(0,600),xaxp=c(0,600,12),yaxp=c(0,6,20),ylim=c(0,6))
lines(fit,col="black",lwd=1)
lines(fit.low,col="red",lwd=1)
lines(fit.up,col="red",lwd=1)
points(Resultados,col="blue",type="h")
points(Resultados,col="blue",pch=20)
text(Resultados[,1],Resultados[,2]+0.01,col="blue",labels=row.names(Resultados),cex=0.75)

Finally, we intersect the OTUs identified as significant according to LR and coda_glmnet with 3 replicates

Significant.capat=Significant[,c(1,2,3,4,5)]
Significant.capat=cbind(Significant.capat,Cuánto=rowSums(Significant.capat[,3:dim(Significant.capat)[2]]))
Significant.capat=Significant.capat[Significant.capat$Cuánto==2,]

DF.Imp=DF[,Significant.capat[,1]]
HC=ClusterHC(DF.Imp,dendrograma=TRUE,barplot=FALSE,Grups=Type,colores=colors)

There are 60 taxa. They are:

Significant.capat[,1:2]%>%
  kbl() %>%
  kable_styling() 

	OTUs	taxa
OTU4	OTU4	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea;s__bacterium_AMSU
OTU6	OTU6	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maritimimonas;s__uncultured_Bacteroidetes
OTU19	OTU19	d__Bacteria;p__Chloroflexi;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;guncultured;
OTU25	OTU25	d__Archaea;p__Asgardarchaeota;c__Heimdallarchaeia;o__Heimdallarchaeia;f__Heimdallarchaeia;g__Heimdallarchaeia;s__uncultured_archaeon
OTU26	OTU26	d__Bacteria;p__Chloroflexi;c__Anaerolineae;o__SBR1031;f__SBR1031;g__SBR1031;s__uncultured_organism
OTU27	OTU27	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter;s__Aureitalea_sp.
OTU31	OTU31	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;oEctothiorhodospirales;;;
OTU34	OTU34	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;gMaribacter;
OTU48	OTU48	d__Bacteria;p__Patescibacteria;c__Parcubacteria;;;;
OTU56	OTU56	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__Arenicellaceae;guncultured;
OTU78	OTU78	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Spirochaetales;f__Spirochaetaceae;gSpirochaeta;
OTU85	OTU85	d__Bacteria;pChloroflexi;;;;;
OTU94	OTU94	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Spirochaetales;f__Spirochaetaceae;g__Spirochaeta;s__uncultured_bacterium
OTU102	OTU102	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__IheB3-7;s__uncultured_Chlorobi
OTU107	OTU107	d__Bacteria;p__Actinobacteriota;c__WCHB1-81;o__WCHB1-81;f__WCHB1-81;gWCHB1-81;
OTU118	OTU118	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Marine_Benthic_Group_D_and_DHVEG-1;f__Marine_Benthic_Group_D_and_DHVEG-1;g__Marine_Benthic_Group_D_and_DHVEG-1;s__uncultured_archaeon
OTU123	OTU123	d__Bacteria;p__Planctomycetota;c__Planctomycetes;o__Pirellulales;f__Pirellulaceae;gPir4_lineage;
OTU126	OTU126	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;guncultured;
OTU133	OTU133	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfatiglandales;f__Desulfatiglandaceae;gDesulfatiglans;
OTU136	OTU136	d__Bacteria;p__Patescibacteria;c__Parcubacteria;o__Candidatus_Kaiserbacteria;f__Candidatus_Kaiserbacteria;g__Candidatus_Kaiserbacteria;s__uncultured_bacterium
OTU137	OTU137	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Marine_Benthic_Group_D_and_DHVEG-1;f__Marine_Benthic_Group_D_and_DHVEG-1;gMarine_Benthic_Group_D_and_DHVEG-1;
OTU143	OTU143	d__Archaea;p__Crenarchaeota;c__Bathyarchaeia;o__Bathyarchaeia;f__Bathyarchaeia;gBathyarchaeia;
OTU144	OTU144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;gAquibacter;
OTU163	OTU163	d__Bacteria;p__Modulibacteria;c__Moduliflexia;o__Moduliflexales;f__Moduliflexaceae;g__Moduliflexaceae;s__uncultured_bacterium
OTU168	OTU168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;gendosymbionts;
OTU174	OTU174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__SB-5;g__SB-5;s__bacterium_YC-LK-LKJ31
OTU178	OTU178	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;gWinogradskyella;
OTU181	OTU181	d__Bacteria;p__Chloroflexi;c__Anaerolineae;;;;
OTU182	OTU182	d__Bacteria;p__Chloroflexi;c__Anaerolineae;o__uncultured;f__uncultured;guncultured;
OTU186	OTU186	d__Bacteria;p__LCP-89;c__LCP-89;o__LCP-89;f__LCP-89;g__LCP-89;s__uncultured_bacterium
OTU200	OTU200	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;;
OTU212	OTU212	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__uncultured;s__uncultured_bacterium
OTU216	OTU216	d__Bacteria;p__Actinobacteriota;c__WCHB1-81;o__WCHB1-81;f__WCHB1-81;g__WCHB1-81;s__uncultured_bacterium
OTU224	OTU224	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__uncultured;s__uncultured_bacterium
OTU241	OTU241	d__Bacteria;p__Chloroflexi;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__uncultured;s__uncultured_Chloroflexi
OTU283	OTU283	d__Bacteria;p__Calditrichota;c__Calditrichia;o__Calditrichales;f__Calditrichaceae;;
OTU296	OTU296	d__Bacteria;p__Patescibacteria;c__Parcubacteria;o__Candidatus_Kaiserbacteria;f__Candidatus_Kaiserbacteria;g__Candidatus_Kaiserbacteria;s__uncultured_prokaryote
OTU309	OTU309	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;gLewinella;
OTU329	OTU329	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquibacter;s__uncultured_marine
OTU347	OTU347	d__Bacteria;p__Chloroflexi;c__Dehalococcoidia;;;;
OTU372	OTU372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Oceanospirillales;f__Pseudohongiellaceae;gPseudohongiella;
OTU412	OTU412	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;oDesulfobulbales;;;
OTU426	OTU426	d__Bacteria;p__Verrucomicrobiota;c__Omnitrophia;o__Omnitrophales;f__Omnitrophaceae;g__Candidatus_Omnitrophus;s__uncultured_bacterium
OTU433	OTU433	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella;s__uncultured_marine
OTU490	OTU490	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bacteriovoracales;f__Bacteriovoracaceae;gPeredibacter;
OTU516	OTU516	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;gBdellovibrio;
OTU565	OTU565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Portibacter;s__uncultured_Bacteroidetes
OTU574	OTU574	d__Bacteria;p__Planctomycetota;c__Planctomycetes;o__Pirellulales;f__Pirellulaceae;g__uncultured;s__uncultured_organism
OTU597	OTU597	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Thermoanaerobaculales;f__Thermoanaerobaculaceae;g__Subgroup_23;s__uncultured_bacterium
OTU622	OTU622	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__uncultured;g__uncultured;s__uncultured_Bacteroidetes
OTU625	OTU625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__pItb-vmat-80;f__pItb-vmat-80;gpItb-vmat-80;
OTU659	OTU659	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Mitochondria;g__Mitochondria;s__uncultured_bacterium
OTU785	OTU785	d__Archaea;p__Asgardarchaeota;c__Odinarchaeia;o__Odinarchaeia;f__Odinarchaeia;g__Odinarchaeia;s__uncultured_crenarchaeote
OTU854	OTU854	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Puniceicoccaceae;gLentimonas;
OTU980	OTU980	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Phaeodactylibacter;s__uncultured_organism
OTU1088	OTU1088	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cellvibrionales;f__Halieaceae;gCongregibacter;
OTU1502	OTU1502	d__Archaea;p__Thermoplasmatota;c__Thermoplasmatota;o__Thermoplasmatota;f__Thermoplasmatota;guncultured;
OTU1532	OTU1532	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Candidatus_Thiobios;s__uncultured_organism
OTU1539	OTU1539	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Subgroup_17;f__Subgroup_17;gSubgroup_17;
OTU2370	OTU2370	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__uncultured;s__uncultured_deep-sea

The separation between groups is 4.31.

We update the plot with the separations:

intersección=c(dim(Significant.capat)[1],Sep(HC))
Resultados=rbind(Resultados,intersección)
row.names(Resultados)=c(
"LR",
"glmnet.ext.3",
"glmnet.ext.5",
"glmnet.ext.10",
"Aldex",
"simper",
"Intersection")
colnames(Resultados)=c("Size","Separation")

plot(F.SS[-1,c(1,3)],pch=20,cex=0.25,col="darkgrey",xlab="n",ylab="Separation",main="Average separation for perfect classifiers",xlim=c(0,150),xaxp=c(0,150,15),yaxp=c(0,6,12),ylim=c(0,6))
lines(fit,col="black",lwd=1)
lines(fit.low,col="red",lwd=1)
lines(fit.up,col="red",lwd=1)
points(Resultados[-dim(Resultados)[1],],col="blue",type="h")
points(Resultados[-dim(Resultados)[1],],col="blue",pch=20)
points(intersección[1],intersección[2],col="purple",type="h")
points(intersección[1],intersección[2],col="purple",pch=20)
text(Resultados[-dim(Resultados)[1],1],Resultados[-dim(Resultados)[1],2]+0.1,col="blue",labels=row.names(Resultados)[-dim(Resultados)[1]],cex=0.75)
text(intersección[1],intersección[2]+0.1,col="purple",labels="intersección",cex=0.75)

abline(h=base,col="green")
text(20,base+0.1,col="green",labels="Global",cex=0.75)

Resultados %>%
  kbl() %>%
  kable_styling()

	Size	Separation
LR	563	2.150788
glmnet.ext.3	81	3.668474
glmnet.ext.5	84	3.399211
glmnet.ext.10	82	3.085298
Aldex	29	3.114325
simper	120	1.415174
Intersection	60	4.306244

6.8 CAU T0 vs CAU T1

tax_otu=as.data.frame(read_excel("TablaOTUs.xlsx"))[1:12,]

Samples=tax_otu$ID 
taxa=colnames(tax_otu[,3:dim(tax_otu)[2]])
OTUs=paste("OTU",1:(dim(tax_otu)[2]-2),sep="")

DF.0=tax_otu[,-c(1,2)]
row.names(DF.0)=Samples
colnames(DF.0)=OTUs

taxa.original=taxa
DF.0.original=DF.0
n.OTUs.original=dim(DF.0)[2]

Miseria=as.vector(which(colSums(DF.0[1:6,])<=3))
DF.0=DF.0[,-Miseria]
taxa=taxa[-Miseria]
OTUs=OTUs[-Miseria]

hit=function(x){min(c(x,1))}
DF.0.hits=as.matrix(DF.0)
DF.0.hits[]=vapply(DF.0.hits, hit, numeric(1))

Unics=data.frame(
Sample=rep(NA,length(which(colSums(DF.0.hits)==1))), OTUs=names(colSums(DF.0)[which(colSums(DF.0.hits)==1)]), Reads=colSums(DF.0)[which(colSums(DF.0.hits)==1)],
            Proportions=rep(0,length(which(colSums(DF.0.hits)==1)))  
)
for (i in 1:length(Unics$OTUs)){
ii=which(DF.0.hits[,Unics$OTUs[i]]==1)  
Unics$Proportions[i]=DF.0[ii,Unics$OTUs[i]]/sum(DF.0[ii,])
Unics$Sample[i]=Samples[ii]}
Unics.Freqs=Unics[Unics$Proportions>=0.05/100,]
row.names(Unics.Freqs)=NULL


DF.0=DF.0[,-which(colSums(DF.0.hits)==1)]
taxa=taxa[-which(colSums(DF.0.hits)==1)]
OTUs=OTUs[-which(colSums(DF.0.hits)==1)]

row.names(DF.0)=Samples

DF=zCompositions::cmultRepl(DF.0,method="GBM",output="p-counts",suppress.print=TRUE,z.warning=0.99)

DF=DF[1:6,]
DF.0=DF.0[1:6,]
DF.0.original=DF.0.original[1:6 ,]

Type=as.factor(c(rep("CAU_T0", 3),rep("CAU_T1", 3)))
colors=c("blue","green")[Type]

After removing OTUs with 2 or fewer reads across the samples and those appearing in only one of these samples, 1194 taxa remain.

The OTUs removed at this step that represent more than 0.05% of the sample in which they appear are:

Unics.Freqs[rev(order(Unics.Freqs$Proportions)),] %>%
  kbl() %>%
  kable_styling()

Sample	OTUs	Reads	Proportions
CAU_T0_2	OTU966	55	0.0012226

rm(tax_otu)
rm(DF.0.hits)
rm(Miseria)
rm(Unics.Freqs)

6.8.1 How different are the samples?

HC=ClusterHC(DF,Grups=Type,colores=colors)

base=Sep(HC)

The two sample types are not initially separated.

We now examine the proportion of OTU subsets of reasonable size that already classify them correctly.

> initial_seed=as.integer(Sys.time())
> print (initial_seed)
# [1] 1717749309
initial_seed %% 10000
# [1] 9309

set.seed(9309)
Experimento=function(i)
{
  ii=sample(dim(DF)[2],i,rep=FALSE)
  DFtemp=DF[,ii]
  CC=ClusterHC(DFtemp,dendrograma=FALSE,barplot=FALSE, Grups=Type,colores=colors)
  c(Encerts(CC$tabla,table(Type)),Sep(CC))
}
n=500
F.SS=c()
for (i in 10:600) 
  {
  print(i)
  EE=replicate(n,Experimento(i))
  EE.2=EE[2,which(EE[1,]==0)]
  if(length(which(EE[1,]==0))>0){
XX=replicate(1000,mean(sample(EE.2,n,replace=TRUE)))
  F.SS=rbind(F.SS, c(i,
                     length(EE.2)/250,
                      mean(EE.2),
                      quantile(XX,0.025),
                      quantile(XX,0.975)
  ))}
    else {
    F.SS=rbind(F.SS, c(i,
                     0,
                      NA,
                      NA,
                      NA))
  }
  }
colnames(F.SS)=c("n","Proportion","Avg. sep.","Q_0.025","Q_0.975")
saveRDS(F.SS, file="Fraccio.Separadors.CAU.T0vsT1.RData")

F.SS=readRDS("Fraccio.Separadors.CAU.T0vsT1.RData")

The first plot shows, for each \(n\) up to 500, the proportion of samples of size \(n\) that perfectly classify CAU_T0 and CAU_T1 (black curve), along with the 95% Clopper–Pearson confidence interval for that proportion (red curves). We used smoothing splines to smooth the curves.

F.SS_prop.Q_0.025=epitools::binom.exact(F.SS[,2]*250,250)$lower
F.SS_prop.Q_0.975=epitools::binom.exact(F.SS[,2]*250,250)$upper
fit = smooth.spline(F.SS[,1],F.SS[,2],cv=TRUE)
fit.low = smooth.spline(F.SS[,1],F.SS_prop.Q_0.025,cv=TRUE)
fit.up = smooth.spline(F.SS[,1],F.SS_prop.Q_0.975,cv=TRUE)


plot(F.SS[,1:2],pch=20,cex=0.25,col="darkgrey",xlab="n",ylab="Proportion",main="Proportion of perfect classifiers",ylim=c(0,0.1),xlim=c(0,600),xaxp=c(0,600,12),yaxp=c(0,0.1,10))
lines(fit,col="black",lwd=1)
lines(fit.low,col="red",lwd=1)
lines(fit.up,col="red",lwd=1)

The second plot shows, for each \(n\) up to 600, the estimated mean separation obtained with a sample of size \(n\) that perfectly classifies CAU_T0 and CAU_T1 (black curve), along with the 95% confidence interval of this mean separation obtained via bootstrap (red curve).

fit = smooth.spline(F.SS[!is.na(F.SS[,3]),1],F.SS[!is.na(F.SS[,3]),3],cv=TRUE)
fit.low = smooth.spline(F.SS[!is.na(F.SS[,3]),1],F.SS[!is.na(F.SS[,3]),4],cv=TRUE)
fit.up = smooth.spline(F.SS[!is.na(F.SS[,3]),1],F.SS[!is.na(F.SS[,3]),5],cv=TRUE)

plot(F.SS[,c(1,3)],pch=20,cex=0.25,col="darkgrey",xlab="n",ylab="Separation",main="Average separation for perfect classifiers",xlim=c(0,600),xaxp=c(0,600,12),yaxp=c(0,1.5,15))
lines(fit,col="black",lwd=1)
lines(fit.low,col="red",lwd=1)
lines(fit.up,col="red",lwd=1)

`

6.8.2 Taxa with maximum relevant log-ratios

LRS=explore_logratios(DF,Type)
saveRDS(LRS, file="LRS_CAU_T0T1.RData")

LRS=readRDS("LRS_CAU_T0T1.RData")

assoc=rep(0,dim(DF)[2]-4)
for (m in 5:dim(DF)[2]){
    assoc[m-4]=sum(LRS$`association log-ratio with y`[1:m,1:m])/m^2
}

plot(5:dim(DF)[2],assoc,type="b",xlab="m",ylab="Average goodness of the m most relevant." ,pch=20,cex=0.5)

m=4+which.max(assoc)
impLR=sort(as.numeric(LRS$`order of importance`[1:m]))

HC=ClusterHC(DF[,impLR],barplot=FALSE,Grups=Type,colores=colors)

LR.max=c(length(impLR),Sep(HC))

The maximum is attained at the set of 24 most logratio-relevant taxa.
They perfectly separate the two sample types. The separation between groups is 2.3.

Significant=data.frame(
  OTUs=paste("OTU",1:n.OTUs.original,sep=""),
  taxa=taxa.original,
  Log_ratio.max=Indicador(impLR))

6.8.3 Taxa relevant for the bacterial signature (according to coda_glmnet)

coda.glmnet=coda_glmnet(DF,Type,showPlots = FALSE)

## [1] "No variables are selected. The prediction and the signature plots are not displayed."

coda.glmnet$`signature plot`

## NULL

coda_glmnet does not find taxa with significant differences. We add random replicates. We test with 3, 5, and 10 replicates.

> initial_seed=as.integer(Sys.time())
> print (initial_seed)
# [1]  1717764843
initial_seed %% 10000
# [1]  4843

# 3 replicates
set.seed(4843)
M=3
repls=aldexCesc.clr(t(DF), conds=Type, mc.samples=M)@analysisData

## [1] "operating in serial mode"

repls=t(cbind(repls$CAU_T0_1,repls$CAU_T0_2,repls$CAU_T0_3,repls$CAU_T1_1,repls$CAU_T1_2,repls$CAU_T1_3))
attr(repls,"dimnames")[[2]]=NULL
colnames(repls)=colnames(DF)
row.names(repls)=c(paste("CAU_T0_1",1:M,sep="_"),
  paste("CAU_T0_2",1:M,sep="_"),
  paste("CAU_T0_3",1:M,sep="_"),
  paste("CAU_T1_1",1:M,sep="_"),
  paste("CAU_T1_2",1:M,sep="_"),
  paste("CAU_T1_3",1:M,sep="_"))
mostres=rbind(repls,easyCODA::CLR(DF)$LR)
rm(repls)
Type_ext=as.factor(c(rep("CAU_T0", 3*M),rep("CAU_T1", 3*M),rep("CAU_T0", 3),rep("CAU_T1", 3)))
colors_ext=c("blue","green")[Type_ext]

LogRat_mostres=logratios_matrix_clr(mostres)
LogRat_mostres=list(LogRat_mostres[[1]],LogRat_mostres[[2]])
saveRDS(LogRat_mostres, file="LogRat_mostres_CAU_T0T1_3copies.RData")

LogRat_mostres=readRDS("LogRat_mostres_CAU_T0T1_3copies.RData")
coda.glmnet.3=coda_glmnet_lr_bin(LogRat_mostres,Type_ext,DF,showPlots = FALSE)

impGLMNET_ext.3=coda.glmnet.3$taxa.num
HC=ClusterHC(DF[,impGLMNET_ext.3],dendrograma=TRUE,barplot=FALSE,Grups=Type,colores=colors)

glmnet.ext.3=c(length(impGLMNET_ext.3),Sep(HC))

With 3 replicates, 45 significant taxa are found, perfectly separating the two groups, with a separation of 0.95.

Significant=cbind(Significant,
glmnet_sign.ext.3.T0=Indicador(coda.glmnet.3$taxa.num[coda.glmnet.3$`log-contrast coefficients`>0]),
glmnet_sign.ext.3.T1=Indicador(coda.glmnet.3$taxa.num[coda.glmnet.3$`log-contrast coefficients`<0]))

# 5 replicates
set.seed(4843)
M=5
repls=aldexCesc.clr(t(DF), conds=Type, mc.samples=M)@analysisData

## [1] "operating in serial mode"

repls=t(cbind(repls$CAU_T0_1,repls$CAU_T0_2,repls$CAU_T0_3,repls$CAU_T1_1,repls$CAU_T1_2,repls$CAU_T1_3))
attr(repls,"dimnames")[[2]]=NULL
colnames(repls)=colnames(DF)
row.names(repls)=c(paste("CAU_T0_1",1:M,sep="_"),
  paste("CAU_T0_2",1:M,sep="_"),
  paste("CAU_T0_3",1:M,sep="_"),
  paste("CAU_T1_1",1:M,sep="_"),
  paste("CAU_T1_2",1:M,sep="_"),
  paste("CAU_T1_3",1:M,sep="_"))
mostres=rbind(repls,easyCODA::CLR(DF)$LR)
rm(repls)
Type_ext=as.factor(c(rep("CAU_T0", 3*M),rep("CAU_T1", 3*M),rep("CAU_T0", 3),rep("CAU_T1", 3)))
colors_ext=c("blue","green")[Type_ext]

LogRat_mostres=logratios_matrix_clr(mostres)
LogRat_mostres=list(LogRat_mostres[[1]],LogRat_mostres[[2]])
saveRDS(LogRat_mostres, file="LogRat_mostres_CAU_T0T1_5copies.RData")

LogRat_mostres=readRDS("LogRat_mostres_CAU_T0T1_5copies.RData")
coda.glmnet.5=coda_glmnet_lr_bin(LogRat_mostres,Type_ext,DF,showPlots = FALSE)

impGLMNET_ext.5=coda.glmnet.5$taxa.num
HC=ClusterHC(DF[,impGLMNET_ext.5],dendrograma=TRUE,barplot=FALSE,Grups=Type,colores=colors)

glmnet.ext.5=c(length(impGLMNET_ext.5),Sep(HC))

With 5 replicates, 51 significant taxa are found, perfectly separating the two groups, with a separation of 0.88.

Significant=cbind(Significant,
glmnet_sign.ext.5.T0=Indicador(coda.glmnet.5$taxa.num[coda.glmnet.5$`log-contrast coefficients`>0]),
glmnet_sign.ext.5.T1=Indicador(coda.glmnet.5$taxa.num[coda.glmnet.5$`log-contrast coefficients`<0]))

# 10 replicates
set.seed(4843)
M=10
repls=aldexCesc.clr(t(DF), conds=Type, mc.samples=M)@analysisData

## [1] "operating in serial mode"

repls=t(cbind(repls$CAU_T0_1,repls$CAU_T0_2,repls$CAU_T0_3,repls$CAU_T1_1,repls$CAU_T1_2,repls$CAU_T1_3))
attr(repls,"dimnames")[[2]]=NULL
colnames(repls)=colnames(DF)
row.names(repls)=c(paste("CAU_T0_1",1:M,sep="_"),
  paste("CAU_T0_2",1:M,sep="_"),
  paste("CAU_T0_3",1:M,sep="_"),
  paste("CAU_T1_1",1:M,sep="_"),
  paste("CAU_T1_2",1:M,sep="_"),
  paste("CAU_T1_3",1:M,sep="_"))
mostres=rbind(repls,easyCODA::CLR(DF)$LR)
rm(repls)
Type_ext=as.factor(c(rep("CAU_T0", 3*M),rep("CAU_T1", 3*M),rep("CAU_T0", 3),rep("CAU_T1", 3)))
colors_ext=c("blue","green")[Type_ext]

LogRat_mostres=logratios_matrix_clr(mostres)
LogRat_mostres=list(LogRat_mostres[[1]],LogRat_mostres[[2]])
saveRDS(LogRat_mostres, file="LogRat_mostres_CAU_T0T1_10copies.RData")

LogRat_mostres=readRDS("LogRat_mostres_CAU_T0T1_10copies.RData")
coda.glmnet.10=coda_glmnet_lr_bin(LogRat_mostres,Type_ext,DF,showPlots = FALSE)

impGLMNET_ext.10=coda.glmnet.10$taxa.num
HC=ClusterHC(DF[,impGLMNET_ext.10],dendrograma=TRUE,barplot=FALSE,Grups=Type,colores=colors)

glmnet.ext.10=c(length(impGLMNET_ext.10),Sep(HC))

With 10 replicates, 49 significant taxa are found, but they do not classify well the samples.

Significant=cbind(Significant,
glmnet_sign.ext.10.T0=Indicador(coda.glmnet.5$taxa.num[coda.glmnet.10$`log-contrast coefficients`>0]),
glmnet_sign.ext.10.T1=Indicador(coda.glmnet.5$taxa.num[coda.glmnet.10$`log-contrast coefficients`<0]))

6.8.4 OTUs significant according to ALDeX

> initial_seed=as.integer(Sys.time())
> print (initial_seed)
# [1] 1717772151
initial_seed %% 10000
# [1] 2151

set.seed(2151)
repl_kw=aldexCesc.clr(t(DF), conds=Type, mc.samples=1000, verbose=FALSE)
aldex_kw=aldex.kw(repl_kw, verbose=FALSE)
#
saveRDS(aldex_kw, file="aldex_kw_CAU_T0T1.RData")

p.valores_kw=readRDS("aldex_kw_CAU_T0T1.RData") 

length(p.valores_kw[p.valores_kw[,1]<0.05,2])

## [1] 0

There are no taxa with a p-value < 0.05, even without adjustment.

6.9 Simper

The significant taxa identified by simper do not classify the samples well:

DF.prop=DF.0.original/rowSums(DF.0.original)
SMP.prop=simper(DF.prop,group=Type)
indexos_SMP=SMP.prop$CAU_T0_CAU_T1$ord[which(SMP.prop$CAU_T0_CAU_T1$cusum<=0.7)]
OTUs_SMP=sort(attr(SMP.prop$CAU_T0_CAU_T1$cusum[which(SMP.prop$CAU_T0_CAU_T1$cusum<=0.7)],"names"))
OTUs_SMP.good=setdiff(OTUs_SMP,Unics$OTUs)
HC=ClusterHC(DF[,OTUs_SMP.good],dendrograma=TRUE,barplot=FALSE,Grups=Type,colores=colors)

Significant=cbind(Significant,
t(DF.prop))

6.9.1 Summary

write.csv2(Significant,"OTU_Significativos_CAU_T0T1.csv",row.names=FALSE)

Resultados=rbind(
LR.max,
glmnet.ext.3,
glmnet.ext.5,
glmnet.ext.10
)
row.names(Resultados)=c(
"LR",
"glmnet.ext.3",
"glmnet.ext.5",
"glmnet.ext.10")
colnames(Resultados)=c("Size","Separation")

par(opar)
fit = smooth.spline(F.SS[!is.na(F.SS[,3]),1],F.SS[!is.na(F.SS[,3]),3],cv=TRUE)
fit.low = smooth.spline(F.SS[!is.na(F.SS[,3]),1],F.SS[!is.na(F.SS[,3]),4],cv=TRUE)
fit.up = smooth.spline(F.SS[!is.na(F.SS[,3]),1],F.SS[!is.na(F.SS[,3]),5],cv=TRUE)

plot(F.SS[,c(1,3)],pch=20,cex=0.25,col="darkgrey",xlab="n",ylab="Separation",main="Average separation for perfect classifiers",xlim=c(0,650),xaxp=c(0,650,13),ylim=c(0,max(Resultados[,2])+0.1))


lines(fit,col="black",lwd=1)
lines(fit.low,col="red",lwd=1)
lines(fit.up,col="red",lwd=1)
points(Resultados,col="blue",type="h")
points(Resultados,col="blue",pch=20)
text(Resultados[,1],Resultados[,2]+0.01,col="blue",labels=row.names(Resultados),cex=0.75)

We intersect the OTUs identified as significant according to LR and coda_glmnet with 3 replicates

Significant.capat=Significant[,c(1,2,3,4,5)]
Significant.capat=cbind(Significant.capat,Cuánto=rowSums(Significant.capat[,3:dim(Significant.capat)[2]]))
Significant.capat=Significant.capat[Significant.capat$Cuánto==2,]

Significant.capat[,1:2]%>%
  kbl() %>%
  kable_styling() 

	OTUs	taxa
OTU952	OTU952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Beggiatoales;f__Beggiatoaceae;g__Thioflexothrix;s__Thiotrichales_bacterium

A single OTU. The same happens with 5 replicates:

Significant.capat=Significant[,c(1,2,3,6,7)]
Significant.capat=cbind(Significant.capat,Cuánto=rowSums(Significant.capat[,3:dim(Significant.capat)[2]]))
Significant.capat=Significant.capat[Significant.capat$Cuánto==2,]

Significant.capat[,1:2]%>%
  kbl() %>%
  kable_styling() 

	OTUs	taxa
OTU828	OTU828	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Rubritaleaceae;g__Roseibacillus;s__uncultured_organism

Resultados %>%
  kbl() %>%
  kable_styling()

	Size	Separation
LR	24	2.2969800
glmnet.ext.3	45	0.9462113
glmnet.ext.5	51	0.8765157
glmnet.ext.10	49	0.8640208

6.10 CYM T0 vs CYM T1

tax_otu=as.data.frame(read_excel("TablaOTUs.xlsx"))[13:24,]

Samples=tax_otu$ID 
taxa=colnames(tax_otu[,3:dim(tax_otu)[2]])
OTUs=paste("OTU",1:(dim(tax_otu)[2]-2),sep="")

DF.0=tax_otu[,-c(1,2)]
row.names(DF.0)=Samples
colnames(DF.0)=OTUs

taxa.original=taxa
DF.0.original=DF.0
n.OTUs.original=dim(DF.0)[2]

Miseria=as.vector(which(colSums(DF.0[1:6,])<=3))
DF.0=DF.0[,-Miseria]
taxa=taxa[-Miseria]
OTUs=OTUs[-Miseria]

hit=function(x){min(c(x,1))}
DF.0.hits=as.matrix(DF.0)
DF.0.hits[]=vapply(DF.0.hits, hit, numeric(1))

Unics=data.frame(
Sample=rep(NA,length(which(colSums(DF.0.hits)==1))), OTUs=names(colSums(DF.0)[which(colSums(DF.0.hits)==1)]), Reads=colSums(DF.0)[which(colSums(DF.0.hits)==1)],
            Proportions=rep(0,length(which(colSums(DF.0.hits)==1)))  
)
for (i in 1:length(Unics$OTUs)){
ii=which(DF.0.hits[,Unics$OTUs[i]]==1)  
Unics$Proportions[i]=DF.0[ii,Unics$OTUs[i]]/sum(DF.0[ii,])
Unics$Sample[i]=Samples[ii]}
Unics.Freqs=Unics[Unics$Proportions>=0.05/100,]
row.names(Unics.Freqs)=NULL

DF.0=DF.0[,-which(colSums(DF.0.hits)==1)]
taxa=taxa[-which(colSums(DF.0.hits)==1)]
OTUs=OTUs[-which(colSums(DF.0.hits)==1)]

row.names(DF.0)=Samples

DF=zCompositions::cmultRepl(DF.0,method="GBM",output="p-counts",suppress.print=TRUE,z.warning=0.99)

DF=DF[1:6,]
DF.0=DF.0[1:6,]
DF.0.original=DF.0.original[1:6 ,]

Type=as.factor(c(rep("CYM_T0", 3),rep("CYM_T1", 3)))
colors=c("blue","green")[Type]

After removing OTUs with 2 or fewer reads across the samples and those appearing in only one of these samples, 1658 taxa remain.

The OTUs removed at this step that represent more than 0.05% of the sample in which they appear are:

Unics.Freqs[rev(order(Unics.Freqs$Proportions)),] %>%
  kbl() %>%
  kable_styling()

Sample	OTUs	Reads	Proportions

rm(tax_otu)
rm(DF.0.hits)
rm(Miseria)
rm(Unics.Freqs)

6.10.1 How different are the samples?

HC=ClusterHC(DF,Grups=Type,colores=colors)

base=Sep(HC)

The two sample types are not initially separated.

We now examine the proportion of OTU subsets of reasonable size that classify them correctly.

> initial_seed=as.integer(Sys.time())
> print (initial_seed)
# [1] 1717668665
initial_seed %% 10000
# [1] 8665

set.seed(8665)
Experimento=function(i)
{
  ii=sample(dim(DF)[2],i,rep=FALSE)
  DFtemp=DF[,ii]
  CC=ClusterHC(DFtemp,dendrograma=FALSE,barplot=FALSE, Grups=Type,colores=colors)
  c(Encerts(CC$tabla,table(Type)),Sep(CC))
}
n=250
F.SS=c()
for (i in 10:650) #10
  {
  print(i)
  EE=replicate(n,Experimento(i))
  EE.2=EE[2,which(EE[1,]==0)]
  if(length(which(EE[1,]==0))>0){
XX=replicate(1000,mean(sample(EE.2,n,replace=TRUE)))
  F.SS=rbind(F.SS, c(i,
                     length(EE.2)/250,
                      mean(EE.2),
                      quantile(XX,0.025),
                      quantile(XX,0.975)
  ))}
    else {
    F.SS=rbind(F.SS, c(i,
                     0,
                      NA,
                      NA,
                      NA))
  }
  }
colnames(F.SS)=c("n","Proportion","Avg. sep.","Q_0.025","Q_0.975")
saveRDS(F.SS, file="Fraccio.Separadors.CYM.T0vsT1.RData")

F.SS=readRDS("Fraccio.Separadors.CYM.T0vsT1.RData")

The first plot shows, for each \(n\) up to 500, the proportion of samples of size \(n\) that perfectly classify CYM_T0 and CYM_T1 (black curve), along with the 95% Clopper–Pearson confidence interval for that proportion (red curves). We used smoothing splines to smooth the curves.

F.SS_prop.Q_0.025=epitools::binom.exact(F.SS[,2]*250,250)$lower
F.SS_prop.Q_0.975=epitools::binom.exact(F.SS[,2]*250,250)$upper
fit = smooth.spline(F.SS[,1],F.SS[,2],cv=TRUE)
fit.low = smooth.spline(F.SS[,1],F.SS_prop.Q_0.025,cv=TRUE)
fit.up = smooth.spline(F.SS[,1],F.SS_prop.Q_0.975,cv=TRUE)


plot(F.SS[,1:2],pch=20,cex=0.25,col="darkgrey",xlab="n",ylab="Proportion",main="Proportion of perfect classifiers",ylim=c(0,0.1),xlim=c(0,650),xaxp=c(0,650,13),yaxp=c(0,0.1,10))
lines(fit,col="black",lwd=1)
lines(fit.low,col="red",lwd=1)
lines(fit.up,col="red",lwd=1)

The second plot shows, for each \(n\) up to 600, the estimated mean separation obtained with a sample of size \(n\) that perfectly classifies CYM_T0 and CYM_T1 (black curve), along with the 95% confidence interval of this mean separation obtained via bootstrap (red curve).

fit = smooth.spline(F.SS[!is.na(F.SS[,3]),1],F.SS[!is.na(F.SS[,3]),3],cv=TRUE)
fit.low = smooth.spline(F.SS[!is.na(F.SS[,3]),1],F.SS[!is.na(F.SS[,3]),4],cv=TRUE)
fit.up = smooth.spline(F.SS[!is.na(F.SS[,3]),1],F.SS[!is.na(F.SS[,3]),5],cv=TRUE)

plot(F.SS[,c(1,3)],pch=20,cex=0.25,col="darkgrey",xlab="n",ylab="Separation",main="Average separation for perfect classifiers",xlim=c(0,650),xaxp=c(0,650,13),yaxp=c(0,1.5,15))
lines(fit,col="black",lwd=1)
lines(fit.low,col="red",lwd=1)
lines(fit.up,col="red",lwd=1)

`

6.10.2 Taxa with maximum relevant log-ratios

LRS=explore_logratios(DF,Type)
saveRDS(LRS, file="LRS_CYM_T0T1.RData")

LRS=readRDS("LRS_CYM_T0T1.RData")

assoc=rep(0,dim(DF)[2]-4)
for (m in 5:dim(DF)[2]){
    assoc[m-4]=sum(LRS$`association log-ratio with y`[1:m,1:m])/m^2
}

plot(5:dim(DF)[2],assoc,type="b",xlab="m",ylab="Average goodness of the m most relevant." ,pch=20,cex=0.5)

m=4+which.max(assoc)
impLR=sort(as.numeric(LRS$`order of importance`[1:m]))

HC=ClusterHC(DF[,impLR],barplot=FALSE,Grups=Type,colores=colors)

LR.max=c(length(impLR),Sep(HC))

The maximum is attained at the set of 169 most logratio-relevant taxa.
They perfectly separate the two sample types. The separation between groups is 2.46.

Significant=data.frame(
  OTUs=paste("OTU",1:n.OTUs.original,sep=""),
  taxa=taxa.original,
  Log_ratio.max=Indicador(impLR))

6.10.3 Taxa relevant for the bacterial signature (according to coda_glmnet)

coda.glmnet=coda_glmnet(DF,Type,showPlots = FALSE)

## [1] "No variables are selected. The prediction and the signature plots are not displayed."

coda.glmnet$`signature plot`

## NULL

coda_glmnet does not find taxa with significant differences. We add random replicates. We test with 3, 5, and 10 replicates.

> initial_seed=as.integer(Sys.time())
> print (initial_seed)
# [1]  1717709647
initial_seed %% 10000
# [1]  9647

# 3 replicates
set.seed(9647)
M=3
repls=aldexCesc.clr(t(DF), conds=Type, mc.samples=M)@analysisData

## [1] "operating in serial mode"

repls=t(cbind(repls$CYM_T0_1,repls$CYM_T0_2,repls$CYM_T0_3,repls$CYM_T1_1,repls$CYM_T1_2,repls$CYM_T1_3))
attr(repls,"dimnames")[[2]]=NULL
colnames(repls)=colnames(DF)
row.names(repls)=c(paste("CYM_T0_1",1:M,sep="_"),
  paste("CYM_T0_2",1:M,sep="_"),
  paste("CYM_T0_3",1:M,sep="_"),
  paste("CYM_T1_1",1:M,sep="_"),
  paste("CYM_T1_2",1:M,sep="_"),
  paste("CYM_T1_3",1:M,sep="_"))
mostres=rbind(repls,easyCODA::CLR(DF)$LR)
rm(repls)
Type_ext=as.factor(c(rep("CYM_T0", 3*M),rep("CYM_T1", 3*M),rep("CYM_T0", 3),rep("CYM_T1", 3)))
colors_ext=c("blue","green")[Type_ext]

LogRat_mostres=logratios_matrix_clr(mostres)
LogRat_mostres=list(LogRat_mostres[[1]],LogRat_mostres[[2]])
saveRDS(LogRat_mostres, file="LogRat_mostres_CYM_T0T1_3copies.RData")

LogRat_mostres=readRDS("LogRat_mostres_CYM_T0T1_3copies.RData")
coda.glmnet.3=coda_glmnet_lr_bin(LogRat_mostres,Type_ext,DF,showPlots = FALSE)

impGLMNET_ext.3=coda.glmnet.3$taxa.num
HC=ClusterHC(DF[,impGLMNET_ext.3],dendrograma=TRUE,barplot=FALSE,Grups=Type,colores=colors)

glmnet.ext.3=c(length(impGLMNET_ext.3),Sep(HC))

With 3 replicates, 62 significant taxa are found, perfectly separating the two groups, with a separation of 2.05.

Significant=cbind(Significant,
glmnet_sign.ext.3.T0=Indicador(coda.glmnet.5$taxa.num[coda.glmnet.5$`log-contrast coefficients`>0]),
glmnet_sign.ext.3.T1=Indicador(coda.glmnet.5$taxa.num[coda.glmnet.5$`log-contrast coefficients`<0]))

# 5 replicates
set.seed(9647)
M=5
repls=aldexCesc.clr(t(DF), conds=Type, mc.samples=M)@analysisData

## [1] "operating in serial mode"

repls=t(cbind(repls$CYM_T0_1,repls$CYM_T0_2,repls$CYM_T0_3,repls$CYM_T1_1,repls$CYM_T1_2,repls$CYM_T1_3))
attr(repls,"dimnames")[[2]]=NULL
colnames(repls)=colnames(DF)
row.names(repls)=c(paste("CYM_T0_1",1:M,sep="_"),
  paste("CYM_T0_2",1:M,sep="_"),
  paste("CYM_T0_3",1:M,sep="_"),
  paste("CYM_T1_1",1:M,sep="_"),
  paste("CYM_T1_2",1:M,sep="_"),
  paste("CYM_T1_3",1:M,sep="_"))
mostres=rbind(repls,easyCODA::CLR(DF)$LR)
rm(repls)
Type_ext=as.factor(c(rep("CYM_T0", 3*M),rep("CYM_T1", 3*M),rep("CYM_T0", 3),rep("CYM_T1", 3)))
colors_ext=c("blue","green")[Type_ext]

LogRat_mostres=logratios_matrix_clr(mostres)
LogRat_mostres=list(LogRat_mostres[[1]],LogRat_mostres[[2]])
saveRDS(LogRat_mostres, file="LogRat_mostres_CYM_T0T1_5copies.RData")

LogRat_mostres=readRDS("LogRat_mostres_CYM_T0T1_5copies.RData")
coda.glmnet.5=coda_glmnet_lr_bin(LogRat_mostres,Type_ext,DF,showPlots = FALSE)

impGLMNET_ext.5=coda.glmnet.5$taxa.num
HC=ClusterHC(DF[,impGLMNET_ext.5],dendrograma=TRUE,barplot=FALSE,Grups=Type,colores=colors)

glmnet.ext.5=c(length(impGLMNET_ext.5),Sep(HC))

With 5 replicates, 74 significant taxa are found, perfectly separating the two groups, with a separation of 1.36.

Significant=cbind(Significant,
glmnet_sign.ext.5.T0=Indicador(coda.glmnet.5$taxa.num[coda.glmnet.5$`log-contrast coefficients`>0]),
glmnet_sign.ext.5.T1=Indicador(coda.glmnet.5$taxa.num[coda.glmnet.5$`log-contrast coefficients`<0]))

# 10 replicates
set.seed(9647)
M=10
repls=aldexCesc.clr(t(DF), conds=Type, mc.samples=M)@analysisData

## [1] "operating in serial mode"

repls=t(cbind(repls$CYM_T0_1,repls$CYM_T0_2,repls$CYM_T0_3,repls$CYM_T1_1,repls$CYM_T1_2,repls$CYM_T1_3))
attr(repls,"dimnames")[[2]]=NULL
colnames(repls)=colnames(DF)
row.names(repls)=c(paste("CYM_T0_1",1:M,sep="_"),
  paste("CYM_T0_2",1:M,sep="_"),
  paste("CYM_T0_3",1:M,sep="_"),
  paste("CYM_T1_1",1:M,sep="_"),
  paste("CYM_T1_2",1:M,sep="_"),
  paste("CYM_T1_3",1:M,sep="_"))
mostres=rbind(repls,easyCODA::CLR(DF)$LR)
rm(repls)
Type_ext=as.factor(c(rep("CYM_T0", 3*M),rep("CYM_T1", 3*M),rep("CYM_T0", 3),rep("CYM_T1", 3)))
colors_ext=c("blue","green")[Type_ext]

LogRat_mostres=logratios_matrix_clr(mostres)
LogRat_mostres=list(LogRat_mostres[[1]],LogRat_mostres[[2]])
saveRDS(LogRat_mostres, file="LogRat_mostres_CYM_T0T1_10copies.RData")

LogRat_mostres=readRDS("LogRat_mostres_CYM_T0T1_10copies.RData")
coda.glmnet.10=coda_glmnet_lr_bin(LogRat_mostres,Type_ext,DF,showPlots = FALSE)

impGLMNET_ext.10=coda.glmnet.10$taxa.num
HC=ClusterHC(DF[,impGLMNET_ext.10],dendrograma=TRUE,barplot=FALSE,Grups=Type,colores=colors)

glmnet.ext.10=c(length(impGLMNET_ext.10),Sep(HC))

With 10 replicates, 67 significant taxa are found, perfectly separating the two groups, with a separation of 1.26.

Significant=cbind(Significant,
glmnet_sign.ext.10.T0=Indicador(coda.glmnet.10$taxa.num[coda.glmnet.10$`log-contrast coefficients`>0]),
glmnet_sign.ext.10.T1=Indicador(coda.glmnet.10$taxa.num[coda.glmnet.10$`log-contrast coefficients`<0]))

6.10.4 OTUs significant according to ALDeX

> initial_seed=as.integer(Sys.time())
> print (initial_seed)
# [1] 1717738742
initial_seed %% 10000
# [1] 8742

set.seed(8742)
repl_kw=aldexCesc.clr(t(DF), conds=Type, mc.samples=1000, verbose=FALSE)
aldex_kw=aldex.kw(repl_kw, verbose=FALSE)
#
repl_glm=aldexCesc.clr(t(DF), conds=model.matrix(~Type,data.frame(Type)), mc.samples=1000, verbose=FALSE)
aldex_glm=aldex.glm(repl_glm, model.matrix(~Type,data.frame(Type)))
#'
saveRDS(aldex_kw, file="aldex_kw_CYM_T0T1.RData")
saveRDS(aldex_glm, file="aldex_glm_CYM_T0T1.RData")

p.valores_kw=readRDS("aldex_kw_CYM_T0T1.RData") 

length(p.valores_kw[p.valores_kw[,2]<0.05,2])

## [1] 0

length(p.valores_kw[p.valores_kw[,4]<0.05,2])

## [1] 88

length(p.valores_kw[p.valores_kw[,4]<0.01,4])

## [1] 6

There are no OTUs with an adjusted Kruskal–Wallis p-value < 0.05. There are 66 OTUs with an unadjusted p-value < 0.05, but they do not separate the samples well:

sep.kw.noadjust.0.05=QQ.HC.noadjust(p.valores_kw,DF,Type,q=0.05,1,BP=FALSE)

Significant=cbind(Significant,
Aldex.kw.noadjust.0.05=Indicador(sep.kw.noadjust.0.05))

6.10.5 Simper

The significant taxa identified by simper do not classify the samples well:

DF.prop=DF.0.original/rowSums(DF.0.original)
SMP.prop=simper(DF.prop,group=Type)
indexos_SMP=SMP.prop$CYM_T0_CYM_T1$ord[which(SMP.prop$CYM_T0_CYM_T1$cusum<=0.7)]
OTUs_SMP=sort(attr(SMP.prop$CYM_T0_CYM_T1$cusum[which(SMP.prop$CYM_T0_CYM_T1$cusum<=0.7)],"names"))
OTUs_SMP.good=setdiff(OTUs_SMP,Unics$OTUs)
HC=ClusterHC(DF[,OTUs_SMP.good],dendrograma=TRUE,barplot=FALSE,Grups=Type,colores=colors)

Significant=cbind(Significant,
t(DF.prop))

6.10.6 Summary

write.csv2(Significant,"OTU_Significativos_CYM_T0T1.csv",row.names=FALSE)

Resultados=rbind(
LR.max,
glmnet.ext.3,
glmnet.ext.5,
glmnet.ext.10)
row.names(Resultados)=c(
"LR",
"glmnet.ext.3",
"glmnet.ext.5",
"glmnet.ext.10"
)
colnames(Resultados)=c("Size","Separation")

par(opar)
fit = smooth.spline(F.SS[!is.na(F.SS[,3]),1],F.SS[!is.na(F.SS[,3]),3],cv=TRUE)
fit.low = smooth.spline(F.SS[!is.na(F.SS[,3]),1],F.SS[!is.na(F.SS[,3]),4],cv=TRUE)
fit.up = smooth.spline(F.SS[!is.na(F.SS[,3]),1],F.SS[!is.na(F.SS[,3]),5],cv=TRUE)

plot(F.SS[,c(1,3)],pch=20,cex=0.25,col="darkgrey",xlab="n",ylab="Separation",main="Average separation for perfect classifiers",xlim=c(0,650),xaxp=c(0,650,13),ylim=c(0,max(Resultados[,2])+0.1))


lines(fit,col="black",lwd=1)
lines(fit.low,col="red",lwd=1)
lines(fit.up,col="red",lwd=1)
points(Resultados,col="blue",type="h")
points(Resultados,col="blue",pch=20)
text(Resultados[,1],Resultados[,2]+0.01,col="blue",labels=row.names(Resultados),cex=0.75)

We intersect the OTUs identified as significant according to LR and coda_glmnet with 3 replicates.

Significant.capat=Significant[,c(1,2,3,4,5)]
Significant.capat=cbind(Significant.capat,Cuánto=rowSums(Significant.capat[,3:dim(Significant.capat)[2]]))
Significant.capat=Significant.capat[Significant.capat$Cuánto==2,]

DF.Imp=DF[,Significant.capat[,1]]
HC=ClusterHC(DF.Imp,dendrograma=TRUE,barplot=FALSE,Grups=Type,colores=colors)

There are 1 taxa. They are:

Significant.capat[,1:2]%>%
  kbl() %>%
  kable_styling() 

	OTUs	taxa
OTU235	OTU235	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__endosymbionts;s__uncultured_bacterium

The separation between groups is 0.98.

We update the plot with the separations:

intersección=c(dim(Significant.capat)[1],Sep(HC))
Resultados=rbind(Resultados,intersección)
row.names(Resultados)=c(
"LR",
"glmnet.ext.3",
"glmnet.ext.5",
"glmnet.ext.10",
"intersection")
colnames(Resultados)=c("Size","Separation")

par(opar)
fit = smooth.spline(F.SS[!is.na(F.SS[,3]),1],F.SS[!is.na(F.SS[,3]),3],cv=TRUE)
fit.low = smooth.spline(F.SS[!is.na(F.SS[,3]),1],F.SS[!is.na(F.SS[,3]),4],cv=TRUE)
fit.up = smooth.spline(F.SS[!is.na(F.SS[,3]),1],F.SS[!is.na(F.SS[,3]),5],cv=TRUE)

plot(F.SS[,c(1,3)],pch=20,cex=0.25,col="darkgrey",xlab="n",ylab="Separation",main="Average separation for perfect classifiers",ylim=c(0,2.25),xlim=c(0,250),xaxp=c(0,250,10),yaxp=c(0,2.5,10))
lines(fit,col="black",lwd=1)
lines(fit.low,col="red",lwd=1)
lines(fit.up,col="red",lwd=1)
points(Resultados,col="blue",type="h")
points(Resultados,col="blue",pch=20)
text(Resultados[,1],Resultados[,2]+0.02,col="blue",labels=row.names(Resultados),cex=0.75)
abline(h=2.47,col="green")
text(20,2.6,col="green",labels="Global",cex=0.75)

Resultados %>%
  kbl() %>%
  kable_styling()